Hugging Face's logo

Datasets:
jglaser
/
binding_affinity

Modalities:
Tabular
Text
Size:
1M - 10M
Tags:
molecules
chemistry
SMILES
Libraries:
Datasets
Dataset card Viewer Files Community
2
jglaser commited on
Commit
fad2eb6
•
1 Parent(s): 9737168

update dataset to only inclulde Ki/Kd (but not IC50/EC50)

Browse files
Files changed (6) hide show
  1. bindingdb.ipynb +289 -31
  2. biolip.ipynb +196 -112
  3. combine_dbs.ipynb +346 -517
  4. data/all.parquet +2 -2
  5. moad.ipynb +193 -96
  6. pdbbind.ipynb +50 -136
bindingdb.ipynb CHANGED
@@ -2,7 +2,7 @@
2
  "cells": [
3
  {
4
  "cell_type": "code",
5
- "execution_count": 1,
6
  "id": "ecce356e-321b-441e-8a5d-a20bf72f8691",
7
  "metadata": {},
8
  "outputs": [],
@@ -12,7 +12,7 @@
12
  },
13
  {
14
  "cell_type": "code",
15
- "execution_count": 2,
16
  "id": "89cbcd82-4ca2-4aba-95b7-e58c0ceed770",
17
  "metadata": {},
18
  "outputs": [],
@@ -22,7 +22,7 @@
22
  },
23
  {
24
  "cell_type": "code",
25
- "execution_count": 3,
26
  "id": "a870d8d7-374b-4474-b9ee-305bbf9f17a9",
27
  "metadata": {},
28
  "outputs": [],
@@ -217,17 +217,17 @@
217
  },
218
  {
219
  "cell_type": "code",
220
- "execution_count": 4,
221
  "id": "d7eafa69-4606-4b34-ae8f-8c6462dcb004",
222
  "metadata": {},
223
  "outputs": [],
224
  "source": [
225
- "ddf = dd.read_parquet('bindingdb/parquet_data/all_targets')"
226
  ]
227
  },
228
  {
229
  "cell_type": "code",
230
- "execution_count": 5,
231
  "id": "b151868a-0cd6-405e-8401-f79918fb0b07",
232
  "metadata": {},
233
  "outputs": [
@@ -340,7 +340,7 @@
340
  "Dask Name: read-parquet, 459 tasks"
341
  ]
342
  },
343
- "execution_count": 5,
344
  "metadata": {},
345
  "output_type": "execute_result"
346
  }
@@ -351,7 +351,7 @@
351
  },
352
  {
353
  "cell_type": "code",
354
- "execution_count": 6,
355
  "id": "c00102b8-f4be-4ebd-8d30-7a2c7fc2d05e",
356
  "metadata": {},
357
  "outputs": [],
@@ -361,7 +361,7 @@
361
  },
362
  {
363
  "cell_type": "code",
364
- "execution_count": 7,
365
  "id": "c5337e06-1e45-4180-90ed-49ac9ecdd24a",
366
  "metadata": {},
367
  "outputs": [
@@ -473,7 +473,7 @@
473
  "4457 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... "
474
  ]
475
  },
476
- "execution_count": 7,
477
  "metadata": {},
478
  "output_type": "execute_result"
479
  }
@@ -484,7 +484,7 @@
484
  },
485
  {
486
  "cell_type": "code",
487
- "execution_count": 8,
488
  "id": "872edb84-3459-43d9-8e0e-e2a6b5d281eb",
489
  "metadata": {},
490
  "outputs": [],
@@ -498,11 +498,12 @@
498
  " ic50, Ki, Kd, ec50 = affinities\n",
499
  "\n",
500
  " vals = []\n",
501
- " try:\n",
502
- " ic50 = ureg(str(ic50)+'nM').m_as(ureg.uM)\n",
503
- " vals.append(ic50)\n",
504
- " except:\n",
505
- " pass\n",
 
506
  "\n",
507
  " try:\n",
508
  " Ki = ureg(str(Ki)+'nM').m_as(ureg.uM)\n",
@@ -516,11 +517,11 @@
516
  " except:\n",
517
  " pass\n",
518
  "\n",
519
- " try:\n",
520
- " ec50 = ureg(str(ec50)+'nM').m_as(ureg.uM)\n",
521
- " vals.append(ec50)\n",
522
- " except:\n",
523
- " pass\n",
524
  "\n",
525
  " if len(vals) > 0:\n",
526
  " vals = np.array(vals)\n",
@@ -531,7 +532,7 @@
531
  },
532
  {
533
  "cell_type": "code",
534
- "execution_count": 9,
535
  "id": "b3cff13c-19b2-4413-a84b-d99062f516a7",
536
  "metadata": {},
537
  "outputs": [],
@@ -569,7 +570,7 @@
569
  },
570
  {
571
  "cell_type": "code",
572
- "execution_count": 12,
573
  "id": "ca9795de-e821-4dc3-a7bf-70ade9e4c7f0",
574
  "metadata": {},
575
  "outputs": [
@@ -589,7 +590,7 @@
589
  },
590
  {
591
  "cell_type": "code",
592
- "execution_count": 13,
593
  "id": "4356a3e2-fede-48e7-a486-343661fe0a0a",
594
  "metadata": {},
595
  "outputs": [],
@@ -600,7 +601,7 @@
600
  },
601
  {
602
  "cell_type": "code",
603
- "execution_count": 15,
604
  "id": "e91c3af8-84a5-42a2-9e25-49cb2f320b0b",
605
  "metadata": {},
606
  "outputs": [],
@@ -610,7 +611,7 @@
610
  },
611
  {
612
  "cell_type": "code",
613
- "execution_count": 18,
614
  "id": "27194288-cf3e-4c30-ad55-3b0998fdf939",
615
  "metadata": {},
616
  "outputs": [
@@ -728,7 +729,7 @@
728
  "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00099 "
729
  ]
730
  },
731
- "execution_count": 18,
732
  "metadata": {},
733
  "output_type": "execute_result"
734
  }
@@ -739,7 +740,7 @@
739
  },
740
  {
741
  "cell_type": "code",
742
- "execution_count": 17,
743
  "id": "603fd298-0aa6-4097-b298-c55db013548c",
744
  "metadata": {},
745
  "outputs": [
@@ -749,7 +750,7 @@
749
  "2391969"
750
  ]
751
  },
752
- "execution_count": 17,
753
  "metadata": {},
754
  "output_type": "execute_result"
755
  }
@@ -760,10 +761,267 @@
760
  },
761
  {
762
  "cell_type": "code",
763
- "execution_count": null,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
764
  "id": "c6ea5a79-facf-4a50-9d7c-2e1864ebad3d",
765
  "metadata": {},
766
  "outputs": [],
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
767
  "source": []
768
  }
769
  ],
@@ -783,7 +1041,7 @@
783
  "name": "python",
784
  "nbconvert_exporter": "python",
785
  "pygments_lexer": "ipython3",
786
- "version": "3.8.10"
787
  }
788
  },
789
  "nbformat": 4,
 
2
  "cells": [
3
  {
4
  "cell_type": "code",
5
+ "execution_count": 6,
6
  "id": "ecce356e-321b-441e-8a5d-a20bf72f8691",
7
  "metadata": {},
8
  "outputs": [],
 
12
  },
13
  {
14
  "cell_type": "code",
15
+ "execution_count": 7,
16
  "id": "89cbcd82-4ca2-4aba-95b7-e58c0ceed770",
17
  "metadata": {},
18
  "outputs": [],
 
22
  },
23
  {
24
  "cell_type": "code",
25
+ "execution_count": 8,
26
  "id": "a870d8d7-374b-4474-b9ee-305bbf9f17a9",
27
  "metadata": {},
28
  "outputs": [],
 
217
  },
218
  {
219
  "cell_type": "code",
220
+ "execution_count": 10,
221
  "id": "d7eafa69-4606-4b34-ae8f-8c6462dcb004",
222
  "metadata": {},
223
  "outputs": [],
224
  "source": [
225
+ "ddf = dd.read_parquet('../binding_datasets/bindingdb/parquet_data/all_targets')"
226
  ]
227
  },
228
  {
229
  "cell_type": "code",
230
+ "execution_count": 11,
231
  "id": "b151868a-0cd6-405e-8401-f79918fb0b07",
232
  "metadata": {},
233
  "outputs": [
 
340
  "Dask Name: read-parquet, 459 tasks"
341
  ]
342
  },
343
+ "execution_count": 11,
344
  "metadata": {},
345
  "output_type": "execute_result"
346
  }
 
351
  },
352
  {
353
  "cell_type": "code",
354
+ "execution_count": 12,
355
  "id": "c00102b8-f4be-4ebd-8d30-7a2c7fc2d05e",
356
  "metadata": {},
357
  "outputs": [],
 
361
  },
362
  {
363
  "cell_type": "code",
364
+ "execution_count": 13,
365
  "id": "c5337e06-1e45-4180-90ed-49ac9ecdd24a",
366
  "metadata": {},
367
  "outputs": [
 
473
  "4457 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... "
474
  ]
475
  },
476
+ "execution_count": 13,
477
  "metadata": {},
478
  "output_type": "execute_result"
479
  }
 
484
  },
485
  {
486
  "cell_type": "code",
487
+ "execution_count": 21,
488
  "id": "872edb84-3459-43d9-8e0e-e2a6b5d281eb",
489
  "metadata": {},
490
  "outputs": [],
 
498
  " ic50, Ki, Kd, ec50 = affinities\n",
499
  "\n",
500
  " vals = []\n",
501
+ " \n",
502
+ "# try:\n",
503
+ "# ic50 = ureg(str(ic50)+'nM').m_as(ureg.uM)\n",
504
+ "# vals.append(ic50)\n",
505
+ "# except:\n",
506
+ "# pass\n",
507
  "\n",
508
  " try:\n",
509
  " Ki = ureg(str(Ki)+'nM').m_as(ureg.uM)\n",
 
517
  " except:\n",
518
  " pass\n",
519
  "\n",
520
+ "# try:\n",
521
+ "# ec50 = ureg(str(ec50)+'nM').m_as(ureg.uM)\n",
522
+ "# vals.append(ec50)\n",
523
+ "# except:\n",
524
+ "# pass\n",
525
  "\n",
526
  " if len(vals) > 0:\n",
527
  " vals = np.array(vals)\n",
 
532
  },
533
  {
534
  "cell_type": "code",
535
+ "execution_count": 15,
536
  "id": "b3cff13c-19b2-4413-a84b-d99062f516a7",
537
  "metadata": {},
538
  "outputs": [],
 
570
  },
571
  {
572
  "cell_type": "code",
573
+ "execution_count": 16,
574
  "id": "ca9795de-e821-4dc3-a7bf-70ade9e4c7f0",
575
  "metadata": {},
576
  "outputs": [
 
590
  },
591
  {
592
  "cell_type": "code",
593
+ "execution_count": 22,
594
  "id": "4356a3e2-fede-48e7-a486-343661fe0a0a",
595
  "metadata": {},
596
  "outputs": [],
 
601
  },
602
  {
603
  "cell_type": "code",
604
+ "execution_count": 23,
605
  "id": "e91c3af8-84a5-42a2-9e25-49cb2f320b0b",
606
  "metadata": {},
607
  "outputs": [],
 
611
  },
612
  {
613
  "cell_type": "code",
614
+ "execution_count": 26,
615
  "id": "27194288-cf3e-4c30-ad55-3b0998fdf939",
616
  "metadata": {},
617
  "outputs": [
 
729
  "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00099 "
730
  ]
731
  },
732
+ "execution_count": 26,
733
  "metadata": {},
734
  "output_type": "execute_result"
735
  }
 
740
  },
741
  {
742
  "cell_type": "code",
743
+ "execution_count": 27,
744
  "id": "603fd298-0aa6-4097-b298-c55db013548c",
745
  "metadata": {},
746
  "outputs": [
 
750
  "2391969"
751
  ]
752
  },
753
+ "execution_count": 27,
754
  "metadata": {},
755
  "output_type": "execute_result"
756
  }
 
761
  },
762
  {
763
  "cell_type": "code",
764
+ "execution_count": 28,
765
+ "id": "d95ad9a9-d4ca-4679-8a33-235fe6e7047f",
766
+ "metadata": {},
767
+ "outputs": [
768
+ {
769
+ "data": {
770
+ "text/plain": [
771
+ "632297"
772
+ ]
773
+ },
774
+ "execution_count": 28,
775
+ "metadata": {},
776
+ "output_type": "execute_result"
777
+ }
778
+ ],
779
+ "source": [
780
+ "len(df_affinity[~df_affinity['affinity_uM'].isnull()])"
781
+ ]
782
+ },
783
+ {
784
+ "cell_type": "code",
785
+ "execution_count": 29,
786
+ "id": "c3f357f6-e9bc-4a9c-ad11-8f90d609c02b",
787
+ "metadata": {},
788
+ "outputs": [],
789
+ "source": [
790
+ "import pandas as pd"
791
+ ]
792
+ },
793
+ {
794
+ "cell_type": "code",
795
+ "execution_count": 4,
796
  "id": "c6ea5a79-facf-4a50-9d7c-2e1864ebad3d",
797
  "metadata": {},
798
  "outputs": [],
799
+ "source": [
800
+ "df_affinity = pd.read_parquet('../binding_datasets/data/bindingdb.parquet')"
801
+ ]
802
+ },
803
+ {
804
+ "cell_type": "code",
805
+ "execution_count": 5,
806
+ "id": "587da244-1913-4883-9b22-254fd94e53b6",
807
+ "metadata": {},
808
+ "outputs": [
809
+ {
810
+ "data": {
811
+ "text/html": [
812
+ "<div>\n",
813
+ "<style scoped>\n",
814
+ " .dataframe tbody tr th:only-of-type {\n",
815
+ " vertical-align: middle;\n",
816
+ " }\n",
817
+ "\n",
818
+ " .dataframe tbody tr th {\n",
819
+ " vertical-align: top;\n",
820
+ " }\n",
821
+ "\n",
822
+ " .dataframe thead th {\n",
823
+ " text-align: right;\n",
824
+ " }\n",
825
+ "</style>\n",
826
+ "<table border=\"1\" class=\"dataframe\">\n",
827
+ " <thead>\n",
828
+ " <tr style=\"text-align: right;\">\n",
829
+ " <th></th>\n",
830
+ " <th>Ligand SMILES</th>\n",
831
+ " <th>IC50 (nM)</th>\n",
832
+ " <th>KEGG ID of Ligand</th>\n",
833
+ " <th>Ki (nM)</th>\n",
834
+ " <th>Kd (nM)</th>\n",
835
+ " <th>EC50 (nM)</th>\n",
836
+ " <th>seq</th>\n",
837
+ " <th>affinity_uM</th>\n",
838
+ " </tr>\n",
839
+ " </thead>\n",
840
+ " <tbody>\n",
841
+ " <tr>\n",
842
+ " <th>0</th>\n",
843
+ " <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
844
+ " <td>None</td>\n",
845
+ " <td>None</td>\n",
846
+ " <td>0.24</td>\n",
847
+ " <td>None</td>\n",
848
+ " <td>None</td>\n",
849
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
850
+ " <td>0.00024</td>\n",
851
+ " </tr>\n",
852
+ " <tr>\n",
853
+ " <th>1</th>\n",
854
+ " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn...</td>\n",
855
+ " <td>None</td>\n",
856
+ " <td>None</td>\n",
857
+ " <td>0.25</td>\n",
858
+ " <td>None</td>\n",
859
+ " <td>None</td>\n",
860
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
861
+ " <td>0.00025</td>\n",
862
+ " </tr>\n",
863
+ " <tr>\n",
864
+ " <th>2</th>\n",
865
+ " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=...</td>\n",
866
+ " <td>None</td>\n",
867
+ " <td>None</td>\n",
868
+ " <td>0.41</td>\n",
869
+ " <td>None</td>\n",
870
+ " <td>None</td>\n",
871
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
872
+ " <td>0.00041</td>\n",
873
+ " </tr>\n",
874
+ " <tr>\n",
875
+ " <th>3</th>\n",
876
+ " <td>OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@...</td>\n",
877
+ " <td>None</td>\n",
878
+ " <td>None</td>\n",
879
+ " <td>0.8</td>\n",
880
+ " <td>None</td>\n",
881
+ " <td>None</td>\n",
882
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
883
+ " <td>0.00080</td>\n",
884
+ " </tr>\n",
885
+ " <tr>\n",
886
+ " <th>4</th>\n",
887
+ " <td>OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H...</td>\n",
888
+ " <td>None</td>\n",
889
+ " <td>None</td>\n",
890
+ " <td>0.99</td>\n",
891
+ " <td>None</td>\n",
892
+ " <td>None</td>\n",
893
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
894
+ " <td>0.00099</td>\n",
895
+ " </tr>\n",
896
+ " <tr>\n",
897
+ " <th>...</th>\n",
898
+ " <td>...</td>\n",
899
+ " <td>...</td>\n",
900
+ " <td>...</td>\n",
901
+ " <td>...</td>\n",
902
+ " <td>...</td>\n",
903
+ " <td>...</td>\n",
904
+ " <td>...</td>\n",
905
+ " <td>...</td>\n",
906
+ " </tr>\n",
907
+ " <tr>\n",
908
+ " <th>4453</th>\n",
909
+ " <td>CC(C)C[C@H](NC(=O)N1CCC(CC1)C(=O)Nc1ccc(cc1)-c...</td>\n",
910
+ " <td>9.4</td>\n",
911
+ " <td>None</td>\n",
912
+ " <td>None</td>\n",
913
+ " <td>None</td>\n",
914
+ " <td>None</td>\n",
915
+ " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
916
+ " <td>0.00940</td>\n",
917
+ " </tr>\n",
918
+ " <tr>\n",
919
+ " <th>4454</th>\n",
920
+ " <td>CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cncc...</td>\n",
921
+ " <td>11</td>\n",
922
+ " <td>None</td>\n",
923
+ " <td>None</td>\n",
924
+ " <td>None</td>\n",
925
+ " <td>None</td>\n",
926
+ " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
927
+ " <td>0.01100</td>\n",
928
+ " </tr>\n",
929
+ " <tr>\n",
930
+ " <th>4455</th>\n",
931
+ " <td>CC(C)C[C@H](NC(=O)N1CCCC(C1)C(=O)Nc1cnccn1)C(=...</td>\n",
932
+ " <td>355</td>\n",
933
+ " <td>None</td>\n",
934
+ " <td>None</td>\n",
935
+ " <td>None</td>\n",
936
+ " <td>None</td>\n",
937
+ " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
938
+ " <td>0.35500</td>\n",
939
+ " </tr>\n",
940
+ " <tr>\n",
941
+ " <th>4456</th>\n",
942
+ " <td>COc1ccc(NC(=O)N2CCC(CC2)C(=O)N[C@@H](CC(C)C)C(...</td>\n",
943
+ " <td>17</td>\n",
944
+ " <td>None</td>\n",
945
+ " <td>None</td>\n",
946
+ " <td>None</td>\n",
947
+ " <td>None</td>\n",
948
+ " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
949
+ " <td>0.01700</td>\n",
950
+ " </tr>\n",
951
+ " <tr>\n",
952
+ " <th>4457</th>\n",
953
+ " <td>CC(C)C[C@H](NC(=O)C1CCN(CC1)C(=O)Nc1cnccn1)C(=...</td>\n",
954
+ " <td>76</td>\n",
955
+ " <td>None</td>\n",
956
+ " <td>None</td>\n",
957
+ " <td>None</td>\n",
958
+ " <td>None</td>\n",
959
+ " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
960
+ " <td>0.07600</td>\n",
961
+ " </tr>\n",
962
+ " </tbody>\n",
963
+ "</table>\n",
964
+ "<p>2389700 rows × 8 columns</p>\n",
965
+ "</div>"
966
+ ],
967
+ "text/plain": [
968
+ " Ligand SMILES IC50 (nM) \\\n",
969
+ "0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 None \n",
970
+ "1 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn... None \n",
971
+ "2 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=... None \n",
972
+ "3 OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@... None \n",
973
+ "4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... None \n",
974
+ "... ... ... \n",
975
+ "4453 CC(C)C[C@H](NC(=O)N1CCC(CC1)C(=O)Nc1ccc(cc1)-c... 9.4 \n",
976
+ "4454 CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cncc... 11 \n",
977
+ "4455 CC(C)C[C@H](NC(=O)N1CCCC(C1)C(=O)Nc1cnccn1)C(=... 355 \n",
978
+ "4456 COc1ccc(NC(=O)N2CCC(CC2)C(=O)N[C@@H](CC(C)C)C(... 17 \n",
979
+ "4457 CC(C)C[C@H](NC(=O)C1CCN(CC1)C(=O)Nc1cnccn1)C(=... 76 \n",
980
+ "\n",
981
+ " KEGG ID of Ligand Ki (nM) Kd (nM) EC50 (nM) \\\n",
982
+ "0 None 0.24 None None \n",
983
+ "1 None 0.25 None None \n",
984
+ "2 None 0.41 None None \n",
985
+ "3 None 0.8 None None \n",
986
+ "4 None 0.99 None None \n",
987
+ "... ... ... ... ... \n",
988
+ "4453 None None None None \n",
989
+ "4454 None None None None \n",
990
+ "4455 None None None None \n",
991
+ "4456 None None None None \n",
992
+ "4457 None None None None \n",
993
+ "\n",
994
+ " seq affinity_uM \n",
995
+ "0 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00024 \n",
996
+ "1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00025 \n",
997
+ "2 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00041 \n",
998
+ "3 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00080 \n",
999
+ "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00099 \n",
1000
+ "... ... ... \n",
1001
+ "4453 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.00940 \n",
1002
+ "4454 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.01100 \n",
1003
+ "4455 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.35500 \n",
1004
+ "4456 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.01700 \n",
1005
+ "4457 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.07600 \n",
1006
+ "\n",
1007
+ "[2389700 rows x 8 columns]"
1008
+ ]
1009
+ },
1010
+ "execution_count": 5,
1011
+ "metadata": {},
1012
+ "output_type": "execute_result"
1013
+ }
1014
+ ],
1015
+ "source": [
1016
+ "df_affinity"
1017
+ ]
1018
+ },
1019
+ {
1020
+ "cell_type": "code",
1021
+ "execution_count": null,
1022
+ "id": "372a8c60-e63c-4d6a-a144-3ab5f4d93d22",
1023
+ "metadata": {},
1024
+ "outputs": [],
1025
  "source": []
1026
  }
1027
  ],
 
1041
  "name": "python",
1042
  "nbconvert_exporter": "python",
1043
  "pygments_lexer": "ipython3",
1044
+ "version": "3.9.4"
1045
  }
1046
  },
1047
  "nbformat": 4,
biolip.ipynb CHANGED
@@ -23,7 +23,7 @@
23
  },
24
  {
25
  "cell_type": "code",
26
- "execution_count": 3,
27
  "id": "3b59cfb4-c42a-425d-9653-44f07f9e864e",
28
  "metadata": {},
29
  "outputs": [],
@@ -36,7 +36,7 @@
36
  },
37
  {
38
  "cell_type": "code",
39
- "execution_count": 4,
40
  "id": "01123edd-2b98-4fcc-a2e9-28213b9bed82",
41
  "metadata": {},
42
  "outputs": [],
@@ -47,7 +47,7 @@
47
  },
48
  {
49
  "cell_type": "code",
50
- "execution_count": 5,
51
  "id": "bd8671da-66ad-40ad-b221-e33228be65f4",
52
  "metadata": {},
53
  "outputs": [],
@@ -57,7 +57,7 @@
57
  },
58
  {
59
  "cell_type": "code",
60
- "execution_count": 97,
61
  "id": "08b04d75-c01e-4b26-ae2d-622efae3bd1f",
62
  "metadata": {},
63
  "outputs": [],
@@ -68,7 +68,7 @@
68
  },
69
  {
70
  "cell_type": "code",
71
- "execution_count": 98,
72
  "id": "97af5533-10fe-4419-a998-ed80b7d26690",
73
  "metadata": {},
74
  "outputs": [],
@@ -78,35 +78,98 @@
78
  "import re\n",
79
  "ureg = UnitRegistry()\n",
80
  "\n",
 
 
 
81
  "def to_uM(affinities):\n",
82
  " lit, moad, pdbbind, bindingdb = affinities\n",
83
  "\n",
84
  " vals = []\n",
85
  " try:\n",
86
- " lit = re.split('[=~<>]',str(lit))[1].split(' ')[0]\n",
87
- " lit = ureg(lit).m_as(ureg.uM)\n",
88
- " vals.append(lit)\n",
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
89
  " except:\n",
90
  " pass\n",
91
  "\n",
92
  " try:\n",
93
- " moad = re.split('[=~<>]',str(moad))[1].split(' ')[0]\n",
94
- " moad = ureg(moad).m_as(ureg.uM)\n",
95
- " vals.append(moad)\n",
 
 
 
 
96
  " except:\n",
97
  " pass\n",
98
  "\n",
99
  " try:\n",
100
- " pdbbind = re.split('[=~<>]',str(pdbbind))[1].split(' ')[0]\n",
101
- " pdbbind = ureg(bindingdb).m_as(ureg.uM)\n",
102
- " vals.append(pdbbind)\n",
 
 
 
 
103
  " except:\n",
104
  " pass\n",
105
  "\n",
106
  " try:\n",
107
- " bindingdb = re.split('[=~<>]',str(bindingdb))[1].split(' ')[0]\n",
108
- " bindingdb = ureg(bindingdb).m_as(ureg.uM)\n",
109
- " vals.append(bindingdb)\n",
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
110
  " except:\n",
111
  " pass\n",
112
  "\n",
@@ -119,7 +182,7 @@
119
  },
120
  {
121
  "cell_type": "code",
122
- "execution_count": 99,
123
  "id": "e21154a9-d3a0-4aa3-986f-cfeebc280da6",
124
  "metadata": {},
125
  "outputs": [],
@@ -129,7 +192,28 @@
129
  },
130
  {
131
  "cell_type": "code",
132
- "execution_count": 101,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
133
  "id": "0fc94de0-823d-4f4f-9904-1c4d1e722c2e",
134
  "metadata": {},
135
  "outputs": [
@@ -182,7 +266,7 @@
182
  " <td>PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...</td>\n",
183
  " <td>biolip/data/ligand_nr/11gs_EAA_A_1.pdb</td>\n",
184
  " <td>CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C</td>\n",
185
- " <td>1.500</td>\n",
186
  " </tr>\n",
187
  " <tr>\n",
188
  " <th>43</th>\n",
@@ -197,7 +281,22 @@
197
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
198
  " <td>biolip/data/ligand_nr/13gs_SAS_A_1.pdb</td>\n",
199
  " <td>OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c...</td>\n",
200
- " <td>24.000</td>\n",
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
201
  " </tr>\n",
202
  " <tr>\n",
203
  " <th>54</th>\n",
@@ -212,7 +311,7 @@
212
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
213
  " <td>biolip/data/ligand_nr/17gs_GTX_A_1.pdb</td>\n",
214
  " <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",
215
- " <td>10.000</td>\n",
216
  " </tr>\n",
217
  " <tr>\n",
218
  " <th>55</th>\n",
@@ -227,22 +326,7 @@
227
  " <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
228
  " <td>biolip/data/ligand_nr/181l_BNZ_A_1.pdb</td>\n",
229
  " <td>c1ccccc1</td>\n",
230
- " <td>175.000</td>\n",
231
- " </tr>\n",
232
- " <tr>\n",
233
- " <th>56</th>\n",
234
- " <td>182l</td>\n",
235
- " <td>BZF</td>\n",
236
- " <td>A</td>\n",
237
- " <td>1</td>\n",
238
- " <td>None</td>\n",
239
- " <td>Ka=8900M^-1 (BZF)</td>\n",
240
- " <td>None</td>\n",
241
- " <td>Kd=112000nM</td>\n",
242
- " <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
243
- " <td>biolip/data/ligand_nr/182l_BZF_A_1.pdb</td>\n",
244
- " <td>c1ccc2c(c1)occ2</td>\n",
245
- " <td>112.000</td>\n",
246
  " </tr>\n",
247
  " <tr>\n",
248
  " <th>...</th>\n",
@@ -260,49 +344,34 @@
260
  " <td>...</td>\n",
261
  " </tr>\n",
262
  " <tr>\n",
263
- " <th>105087</th>\n",
264
- " <td>8kme</td>\n",
265
- " <td>III</td>\n",
266
- " <td>3</td>\n",
267
- " <td>1</td>\n",
268
- " <td>None</td>\n",
269
- " <td>ki=8uM (BNN CUC TRG LEU PRO)</td>\n",
270
- " <td>None</td>\n",
271
- " <td>None</td>\n",
272
- " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
273
- " <td>biolip/data/ligand_nr/8kme_III_3_1.pdb</td>\n",
274
- " <td>O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(...</td>\n",
275
- " <td>8.000</td>\n",
276
- " </tr>\n",
277
- " <tr>\n",
278
- " <th>105088</th>\n",
279
- " <td>8kme</td>\n",
280
- " <td>III</td>\n",
281
- " <td>4</td>\n",
282
  " <td>1</td>\n",
283
  " <td>None</td>\n",
284
- " <td>ki=8uM (BNN CUC TRG LEU PRO)</td>\n",
285
  " <td>None</td>\n",
 
286
  " <td>None</td>\n",
287
- " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
288
- " <td>biolip/data/ligand_nr/8kme_III_4_1.pdb</td>\n",
289
- " <td>CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H...</td>\n",
290
- " <td>8.000</td>\n",
291
  " </tr>\n",
292
  " <tr>\n",
293
- " <th>105106</th>\n",
294
- " <td>966c</td>\n",
295
- " <td>RS2</td>\n",
296
  " <td>A</td>\n",
297
  " <td>1</td>\n",
298
  " <td>None</td>\n",
299
- " <td>ki=23nM (RS2)</td>\n",
300
- " <td>Ki=23nM (RS2)</td>\n",
301
  " <td>None</td>\n",
302
- " <td>RWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVS...</td>\n",
303
- " <td>biolip/data/ligand_nr/966c_RS2_A_1.pdb</td>\n",
304
- " <td>ONC(=O)CC1(CCOCC1)S(=O)(=O)c1ccc(cc1)Oc1ccccc1</td>\n",
305
- " <td>0.023</td>\n",
 
 
306
  " </tr>\n",
307
  " <tr>\n",
308
  " <th>105124</th>\n",
@@ -317,7 +386,22 @@
317
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
318
  " <td>biolip/data/ligand_nr/9icd_NAP_A_1.pdb</td>\n",
319
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
320
- " <td>125.000</td>\n",
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
321
  " </tr>\n",
322
  " <tr>\n",
323
  " <th>105138</th>\n",
@@ -332,83 +416,83 @@
332
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
333
  " <td>biolip/data/ligand_nr/9nse_ISU_B_2.pdb</td>\n",
334
  " <td>CC[Se]C(=N)N</td>\n",
335
- " <td>0.039</td>\n",
336
  " </tr>\n",
337
  " </tbody>\n",
338
  "</table>\n",
339
- "<p>7588 rows × 12 columns</p>\n",
340
  "</div>"
341
  ],
342
  "text/plain": [
343
- " pdb chain l_id l_chain affinity_lit affinity_moad \\\n",
344
- "38 11gs EAA A 1 None ki=1.5uM (GTT EAA) \n",
345
- "43 13gs SAS A 1 None ki=24uM (SAS) \n",
346
- "54 17gs GTX A 1 None None \n",
347
- "55 181l BNZ A 1 None Ka=5700M^-1 (BNZ) \n",
348
- "56 182l BZF A 1 None Ka=8900M^-1 (BZF) \n",
349
- "... ... ... ... ... ... ... \n",
350
- "105087 8kme III 3 1 None ki=8uM (BNN CUC TRG LEU PRO) \n",
351
- "105088 8kme III 4 1 None ki=8uM (BNN CUC TRG LEU PRO) \n",
352
- "105106 966c RS2 A 1 None ki=23nM (RS2) \n",
353
- "105124 9icd NAP A 1 None kd=125uM (NAP) \n",
354
- "105138 9nse ISU B 2 None Ki=0.039uM (ISU) \n",
355
  "\n",
356
  " affinity_pdbbind-cn affinity_bindingdb \\\n",
357
  "38 Ki=1.5uM (GTT-EAA) None \n",
358
  "43 Ki=24uM (SAS) None \n",
 
359
  "54 None Kd=10000nM \n",
360
  "55 None Kd=175000nM \n",
361
- "56 None Kd=112000nM \n",
362
  "... ... ... \n",
363
- "105087 None None \n",
364
- "105088 None None \n",
365
- "105106 Ki=23nM (RS2) None \n",
366
  "105124 Kd=125uM (NAP) None \n",
 
367
  "105138 None None \n",
368
  "\n",
369
  " seq \\\n",
370
  "38 PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC... \n",
371
  "43 MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA... \n",
 
372
  "54 MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA... \n",
373
  "55 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL... \n",
374
- "56 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL... \n",
375
  "... ... \n",
376
- "105087 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
377
- "105088 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
378
- "105106 RWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVS... \n",
379
  "105124 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
 
380
  "105138 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
381
  "\n",
382
  " ligand_fn \\\n",
383
  "38 biolip/data/ligand_nr/11gs_EAA_A_1.pdb \n",
384
  "43 biolip/data/ligand_nr/13gs_SAS_A_1.pdb \n",
 
385
  "54 biolip/data/ligand_nr/17gs_GTX_A_1.pdb \n",
386
  "55 biolip/data/ligand_nr/181l_BNZ_A_1.pdb \n",
387
- "56 biolip/data/ligand_nr/182l_BZF_A_1.pdb \n",
388
  "... ... \n",
389
- "105087 biolip/data/ligand_nr/8kme_III_3_1.pdb \n",
390
- "105088 biolip/data/ligand_nr/8kme_III_4_1.pdb \n",
391
- "105106 biolip/data/ligand_nr/966c_RS2_A_1.pdb \n",
392
  "105124 biolip/data/ligand_nr/9icd_NAP_A_1.pdb \n",
 
393
  "105138 biolip/data/ligand_nr/9nse_ISU_B_2.pdb \n",
394
  "\n",
395
  " smiles affinity_uM \n",
396
- "38 CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C 1.500 \n",
397
- "43 OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c... 24.000 \n",
398
- "54 CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(... 10.000 \n",
399
- "55 c1ccccc1 175.000 \n",
400
- "56 c1ccc2c(c1)occ2 112.000 \n",
401
  "... ... ... \n",
402
- "105087 O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(... 8.000 \n",
403
- "105088 CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H... 8.000 \n",
404
- "105106 ONC(=O)CC1(CCOCC1)S(=O)(=O)c1ccc(cc1)Oc1ccccc1 0.023 \n",
405
- "105124 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.000 \n",
406
- "105138 CC[Se]C(=N)N 0.039 \n",
407
  "\n",
408
- "[7588 rows x 12 columns]"
409
  ]
410
  },
411
- "execution_count": 101,
412
  "metadata": {},
413
  "output_type": "execute_result"
414
  }
@@ -419,7 +503,7 @@
419
  },
420
  {
421
  "cell_type": "code",
422
- "execution_count": 102,
423
  "id": "2b483565-3c99-4c42-b2a9-f7b97cd8e80e",
424
  "metadata": {},
425
  "outputs": [],
@@ -452,7 +536,7 @@
452
  "name": "python",
453
  "nbconvert_exporter": "python",
454
  "pygments_lexer": "ipython3",
455
- "version": "3.8.10"
456
  }
457
  },
458
  "nbformat": 4,
 
23
  },
24
  {
25
  "cell_type": "code",
26
+ "execution_count": 4,
27
  "id": "3b59cfb4-c42a-425d-9653-44f07f9e864e",
28
  "metadata": {},
29
  "outputs": [],
 
36
  },
37
  {
38
  "cell_type": "code",
39
+ "execution_count": 5,
40
  "id": "01123edd-2b98-4fcc-a2e9-28213b9bed82",
41
  "metadata": {},
42
  "outputs": [],
 
47
  },
48
  {
49
  "cell_type": "code",
50
+ "execution_count": 8,
51
  "id": "bd8671da-66ad-40ad-b221-e33228be65f4",
52
  "metadata": {},
53
  "outputs": [],
 
57
  },
58
  {
59
  "cell_type": "code",
60
+ "execution_count": 14,
61
  "id": "08b04d75-c01e-4b26-ae2d-622efae3bd1f",
62
  "metadata": {},
63
  "outputs": [],
 
68
  },
69
  {
70
  "cell_type": "code",
71
+ "execution_count": 62,
72
  "id": "97af5533-10fe-4419-a998-ed80b7d26690",
73
  "metadata": {},
74
  "outputs": [],
 
78
  "import re\n",
79
  "ureg = UnitRegistry()\n",
80
  "\n",
81
+ "quantities = ['ki','kd','ka','k1/2','kb']\n",
82
+ "\n",
83
+ "others = set()\n",
84
  "def to_uM(affinities):\n",
85
  " lit, moad, pdbbind, bindingdb = affinities\n",
86
  "\n",
87
  " vals = []\n",
88
  " try:\n",
89
+ " q = re.split('[=~<>]',str(lit))[0].lower()\n",
90
+ " if q not in quantities:\n",
91
+ " others.add(q)\n",
92
+ " raise\n",
93
+ " val = re.split('[=~<>]',str(lit))[1].split(' ')[0]\n",
94
+ " val = ureg(val).m_as(ureg.uM)\n",
95
+ " vals.append(val)\n",
96
+ " except:\n",
97
+ " pass\n",
98
+ "\n",
99
+ " try:\n",
100
+ " q = re.split('[=~<>]',str(lit))[0].lower()\n",
101
+ " if q not in quantities:\n",
102
+ " others.add(q)\n",
103
+ " raise\n",
104
+ " val = re.split('[=~<>]',str(lit))[1].split(' ')[0]\n",
105
+ " val = ureg(val).m_as(1/ureg.uM)\n",
106
+ " vals.append(1/val)\n",
107
+ " except:\n",
108
+ " pass\n",
109
+ "\n",
110
+ " try:\n",
111
+ " q = re.split('[=~<>]',str(moad))[0].lower()\n",
112
+ " if q not in quantities:\n",
113
+ " others.add(q)\n",
114
+ " raise\n",
115
+ " val = re.split('[=~<>]',str(moad))[1].split(' ')[0]\n",
116
+ " val = ureg(val).m_as(ureg.uM)\n",
117
+ " vals.append(val)\n",
118
+ " except:\n",
119
+ " pass\n",
120
+ "\n",
121
+ " try:\n",
122
+ " q = re.split('[=~<>]',str(moad))[0].lower()\n",
123
+ " if q not in quantities:\n",
124
+ " others.add(q)\n",
125
+ " raise\n",
126
+ " val = re.split('[=~<>]',str(moad))[1].split(' ')[0]\n",
127
+ " val = ureg(val).m_as(1/ureg.uM)\n",
128
+ " vals.append(1/moad)\n",
129
  " except:\n",
130
  " pass\n",
131
  "\n",
132
  " try:\n",
133
+ " q = re.split('[=~<>]',str(pdbbind))[0].lower()\n",
134
+ " if q not in quantities:\n",
135
+ " others.add(q)\n",
136
+ " raise\n",
137
+ " val = re.split('[=~<>]',str(pdbbind))[1].split(' ')[0]\n",
138
+ " val = ureg(val).m_as(ureg.uM)\n",
139
+ " vals.append(val)\n",
140
  " except:\n",
141
  " pass\n",
142
  "\n",
143
  " try:\n",
144
+ " q = re.split('[=~<>]',str(pdbbind))[0].lower()\n",
145
+ " if q not in quantities:\n",
146
+ " others.add(q)\n",
147
+ " raise\n",
148
+ " val = re.split('[=~<>]',str(pdbbind))[1].split(' ')[0]\n",
149
+ " val = ureg(val).m_as(1/ureg.uM)\n",
150
+ " vals.append(1/val)\n",
151
  " except:\n",
152
  " pass\n",
153
  "\n",
154
  " try:\n",
155
+ " q = re.split('[=~<>]',str(bindingdb))[0].lower()\n",
156
+ " if q not in quantities:\n",
157
+ " others.add(q)\n",
158
+ " raise\n",
159
+ " val = re.split('[=~<>]',str(bindingdb))[1].split(' ')[0]\n",
160
+ " val = ureg(val).m_as(ureg.uM)\n",
161
+ " vals.append(val)\n",
162
+ " except:\n",
163
+ " pass\n",
164
+ "\n",
165
+ " try:\n",
166
+ " q = re.split('[=~<>]',str(bindingdb))[0].lower()\n",
167
+ " if q not in quantities:\n",
168
+ " others.add(q)\n",
169
+ " raise\n",
170
+ " val = re.split('[=~<>]',str(bindingdb))[1].split(' ')[0]\n",
171
+ " val = ureg(val).m_as(1/ureg.uM)\n",
172
+ " vals.append(1/val)\n",
173
  " except:\n",
174
  " pass\n",
175
  "\n",
 
182
  },
183
  {
184
  "cell_type": "code",
185
+ "execution_count": 63,
186
  "id": "e21154a9-d3a0-4aa3-986f-cfeebc280da6",
187
  "metadata": {},
188
  "outputs": [],
 
192
  },
193
  {
194
  "cell_type": "code",
195
+ "execution_count": 64,
196
+ "id": "6b9526ec-b134-4ecb-8fea-b493c3fdac22",
197
+ "metadata": {},
198
+ "outputs": [
199
+ {
200
+ "data": {
201
+ "text/plain": [
202
+ "{'deltag', 'deltah', 'ec50', 'ic50', 'km', 'none'}"
203
+ ]
204
+ },
205
+ "execution_count": 64,
206
+ "metadata": {},
207
+ "output_type": "execute_result"
208
+ }
209
+ ],
210
+ "source": [
211
+ "others"
212
+ ]
213
+ },
214
+ {
215
+ "cell_type": "code",
216
+ "execution_count": 65,
217
  "id": "0fc94de0-823d-4f4f-9904-1c4d1e722c2e",
218
  "metadata": {},
219
  "outputs": [
 
266
  " <td>PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...</td>\n",
267
  " <td>biolip/data/ligand_nr/11gs_EAA_A_1.pdb</td>\n",
268
  " <td>CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C</td>\n",
269
+ " <td>1.5000</td>\n",
270
  " </tr>\n",
271
  " <tr>\n",
272
  " <th>43</th>\n",
 
281
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
282
  " <td>biolip/data/ligand_nr/13gs_SAS_A_1.pdb</td>\n",
283
  " <td>OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c...</td>\n",
284
+ " <td>24.0000</td>\n",
285
+ " </tr>\n",
286
+ " <tr>\n",
287
+ " <th>53</th>\n",
288
+ " <td>16pk</td>\n",
289
+ " <td>BIS</td>\n",
290
+ " <td>A</td>\n",
291
+ " <td>1</td>\n",
292
+ " <td>None</td>\n",
293
+ " <td>None</td>\n",
294
+ " <td>Ki=6uM (BIS)</td>\n",
295
+ " <td>None</td>\n",
296
+ " <td>EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKV...</td>\n",
297
+ " <td>biolip/data/ligand_nr/16pk_BIS_A_1.pdb</td>\n",
298
+ " <td>O[C@@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(C(CCCC(P(...</td>\n",
299
+ " <td>6.0000</td>\n",
300
  " </tr>\n",
301
  " <tr>\n",
302
  " <th>54</th>\n",
 
311
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
312
  " <td>biolip/data/ligand_nr/17gs_GTX_A_1.pdb</td>\n",
313
  " <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",
314
+ " <td>10.0000</td>\n",
315
  " </tr>\n",
316
  " <tr>\n",
317
  " <th>55</th>\n",
 
326
  " <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
327
  " <td>biolip/data/ligand_nr/181l_BNZ_A_1.pdb</td>\n",
328
  " <td>c1ccccc1</td>\n",
329
+ " <td>175.0000</td>\n",
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
330
  " </tr>\n",
331
  " <tr>\n",
332
  " <th>...</th>\n",
 
344
  " <td>...</td>\n",
345
  " </tr>\n",
346
  " <tr>\n",
347
+ " <th>105118</th>\n",
348
+ " <td>9hvp</td>\n",
349
+ " <td>0E9</td>\n",
350
+ " <td>A</td>\n",
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
351
  " <td>1</td>\n",
352
  " <td>None</td>\n",
 
353
  " <td>None</td>\n",
354
+ " <td>Ki=4.5nM (5-mer)</td>\n",
355
  " <td>None</td>\n",
356
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
357
+ " <td>biolip/data/ligand_nr/9hvp_0E9_A_1.pdb</td>\n",
358
+ " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
359
+ " <td>0.0045</td>\n",
360
  " </tr>\n",
361
  " <tr>\n",
362
+ " <th>105119</th>\n",
363
+ " <td>9hvp</td>\n",
364
+ " <td>0E9</td>\n",
365
  " <td>A</td>\n",
366
  " <td>1</td>\n",
367
  " <td>None</td>\n",
 
 
368
  " <td>None</td>\n",
369
+ " <td>Ki=4.5nM (5-mer)</td>\n",
370
+ " <td>None</td>\n",
371
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
372
+ " <td>biolip/data/ligand_nr/9hvp_0E9_A_1.pdb</td>\n",
373
+ " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
374
+ " <td>0.0045</td>\n",
375
  " </tr>\n",
376
  " <tr>\n",
377
  " <th>105124</th>\n",
 
386
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
387
  " <td>biolip/data/ligand_nr/9icd_NAP_A_1.pdb</td>\n",
388
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
389
+ " <td>125.0000</td>\n",
390
+ " </tr>\n",
391
+ " <tr>\n",
392
+ " <th>105133</th>\n",
393
+ " <td>9lpr</td>\n",
394
+ " <td>III</td>\n",
395
+ " <td>P</td>\n",
396
+ " <td>1</td>\n",
397
+ " <td>None</td>\n",
398
+ " <td>None</td>\n",
399
+ " <td>Ki=2000nM (4-mer)</td>\n",
400
+ " <td>None</td>\n",
401
+ " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
402
+ " <td>biolip/data/ligand_nr/9lpr_III_P_1.pdb</td>\n",
403
+ " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
404
+ " <td>2.0000</td>\n",
405
  " </tr>\n",
406
  " <tr>\n",
407
  " <th>105138</th>\n",
 
416
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
417
  " <td>biolip/data/ligand_nr/9nse_ISU_B_2.pdb</td>\n",
418
  " <td>CC[Se]C(=N)N</td>\n",
419
+ " <td>0.0390</td>\n",
420
  " </tr>\n",
421
  " </tbody>\n",
422
  "</table>\n",
423
+ "<p>9341 rows × 12 columns</p>\n",
424
  "</div>"
425
  ],
426
  "text/plain": [
427
+ " pdb chain l_id l_chain affinity_lit affinity_moad \\\n",
428
+ "38 11gs EAA A 1 None ki=1.5uM (GTT EAA) \n",
429
+ "43 13gs SAS A 1 None ki=24uM (SAS) \n",
430
+ "53 16pk BIS A 1 None None \n",
431
+ "54 17gs GTX A 1 None None \n",
432
+ "55 181l BNZ A 1 None Ka=5700M^-1 (BNZ) \n",
433
+ "... ... ... ... ... ... ... \n",
434
+ "105118 9hvp 0E9 A 1 None None \n",
435
+ "105119 9hvp 0E9 A 1 None None \n",
436
+ "105124 9icd NAP A 1 None kd=125uM (NAP) \n",
437
+ "105133 9lpr III P 1 None None \n",
438
+ "105138 9nse ISU B 2 None Ki=0.039uM (ISU) \n",
439
  "\n",
440
  " affinity_pdbbind-cn affinity_bindingdb \\\n",
441
  "38 Ki=1.5uM (GTT-EAA) None \n",
442
  "43 Ki=24uM (SAS) None \n",
443
+ "53 Ki=6uM (BIS) None \n",
444
  "54 None Kd=10000nM \n",
445
  "55 None Kd=175000nM \n",
 
446
  "... ... ... \n",
447
+ "105118 Ki=4.5nM (5-mer) None \n",
448
+ "105119 Ki=4.5nM (5-mer) None \n",
 
449
  "105124 Kd=125uM (NAP) None \n",
450
+ "105133 Ki=2000nM (4-mer) None \n",
451
  "105138 None None \n",
452
  "\n",
453
  " seq \\\n",
454
  "38 PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC... \n",
455
  "43 MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA... \n",
456
+ "53 EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKV... \n",
457
  "54 MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA... \n",
458
  "55 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL... \n",
 
459
  "... ... \n",
460
+ "105118 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
461
+ "105119 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
 
462
  "105124 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
463
+ "105133 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
464
  "105138 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
465
  "\n",
466
  " ligand_fn \\\n",
467
  "38 biolip/data/ligand_nr/11gs_EAA_A_1.pdb \n",
468
  "43 biolip/data/ligand_nr/13gs_SAS_A_1.pdb \n",
469
+ "53 biolip/data/ligand_nr/16pk_BIS_A_1.pdb \n",
470
  "54 biolip/data/ligand_nr/17gs_GTX_A_1.pdb \n",
471
  "55 biolip/data/ligand_nr/181l_BNZ_A_1.pdb \n",
 
472
  "... ... \n",
473
+ "105118 biolip/data/ligand_nr/9hvp_0E9_A_1.pdb \n",
474
+ "105119 biolip/data/ligand_nr/9hvp_0E9_A_1.pdb \n",
 
475
  "105124 biolip/data/ligand_nr/9icd_NAP_A_1.pdb \n",
476
+ "105133 biolip/data/ligand_nr/9lpr_III_P_1.pdb \n",
477
  "105138 biolip/data/ligand_nr/9nse_ISU_B_2.pdb \n",
478
  "\n",
479
  " smiles affinity_uM \n",
480
+ "38 CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C 1.5000 \n",
481
+ "43 OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c... 24.0000 \n",
482
+ "53 O[C@@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(C(CCCC(P(... 6.0000 \n",
483
+ "54 CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(... 10.0000 \n",
484
+ "55 c1ccccc1 175.0000 \n",
485
  "... ... ... \n",
486
+ "105118 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
487
+ "105119 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
488
+ "105124 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.0000 \n",
489
+ "105133 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
490
+ "105138 CC[Se]C(=N)N 0.0390 \n",
491
  "\n",
492
+ "[9341 rows x 12 columns]"
493
  ]
494
  },
495
+ "execution_count": 65,
496
  "metadata": {},
497
  "output_type": "execute_result"
498
  }
 
503
  },
504
  {
505
  "cell_type": "code",
506
+ "execution_count": 66,
507
  "id": "2b483565-3c99-4c42-b2a9-f7b97cd8e80e",
508
  "metadata": {},
509
  "outputs": [],
 
536
  "name": "python",
537
  "nbconvert_exporter": "python",
538
  "pygments_lexer": "ipython3",
539
+ "version": "3.9.4"
540
  }
541
  },
542
  "nbformat": 4,
combine_dbs.ipynb CHANGED
@@ -12,7 +12,7 @@
12
  },
13
  {
14
  "cell_type": "code",
15
- "execution_count": 84,
16
  "id": "b0859483-5e19-4280-9f53-0d00a6f22d34",
17
  "metadata": {},
18
  "outputs": [],
@@ -23,7 +23,7 @@
23
  },
24
  {
25
  "cell_type": "code",
26
- "execution_count": 85,
27
  "id": "f30732b7-7444-47ad-84e7-566e7a6f2f8e",
28
  "metadata": {},
29
  "outputs": [
@@ -62,27 +62,27 @@
62
  " </tr>\n",
63
  " <tr>\n",
64
  " <th>1</th>\n",
65
- " <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
66
- " <td>OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...</td>\n",
67
- " <td>500.000</td>\n",
68
  " </tr>\n",
69
  " <tr>\n",
70
  " <th>2</th>\n",
71
- " <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
72
- " <td>COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...</td>\n",
73
- " <td>0.023</td>\n",
74
  " </tr>\n",
75
  " <tr>\n",
76
  " <th>3</th>\n",
77
- " <td>AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...</td>\n",
78
- " <td>OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)[C-](=O)=O)NC...</td>\n",
79
- " <td>6.430</td>\n",
80
  " </tr>\n",
81
  " <tr>\n",
82
  " <th>4</th>\n",
83
- " <td>GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGA...</td>\n",
84
- " <td>O=[C-](=O)[C@@H](NC1=NC(C)(C)Cc2c1cccc2)Cc1ccccc1</td>\n",
85
- " <td>27.200</td>\n",
86
  " </tr>\n",
87
  " </tbody>\n",
88
  "</table>\n",
@@ -91,20 +91,20 @@
91
  "text/plain": [
92
  " seq \\\n",
93
  "0 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",
94
- "1 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n",
95
- "2 VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n",
96
- "3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
97
- "4 GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGA... \n",
98
  "\n",
99
  " smiles affinity_uM \n",
100
  "0 CCCCCCCCCCCCCCCCCCC[C-](=O)=O 0.026 \n",
101
- "1 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.000 \n",
102
- "2 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.023 \n",
103
- "3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)[C-](=O)=O)NC... 6.430 \n",
104
- "4 O=[C-](=O)[C@@H](NC1=NC(C)(C)Cc2c1cccc2)Cc1ccccc1 27.200 "
105
  ]
106
  },
107
- "execution_count": 85,
108
  "metadata": {},
109
  "output_type": "execute_result"
110
  }
@@ -115,7 +115,7 @@
115
  },
116
  {
117
  "cell_type": "code",
118
- "execution_count": 119,
119
  "id": "2787b9fd-3d6f-4ae3-a3ad-d3539b72782b",
120
  "metadata": {},
121
  "outputs": [],
@@ -135,150 +135,7 @@
135
  },
136
  {
137
  "cell_type": "code",
138
- "execution_count": 120,
139
- "id": "84f522d5-aee8-4d0f-9186-2d90bfc62342",
140
- "metadata": {},
141
- "outputs": [
142
- {
143
- "data": {
144
- "text/html": [
145
- "<div>\n",
146
- "<style scoped>\n",
147
- " .dataframe tbody tr th:only-of-type {\n",
148
- " vertical-align: middle;\n",
149
- " }\n",
150
- "\n",
151
- " .dataframe tbody tr th {\n",
152
- " vertical-align: top;\n",
153
- " }\n",
154
- "\n",
155
- " .dataframe thead th {\n",
156
- " text-align: right;\n",
157
- " }\n",
158
- "</style>\n",
159
- "<table border=\"1\" class=\"dataframe\">\n",
160
- " <thead>\n",
161
- " <tr style=\"text-align: right;\">\n",
162
- " <th></th>\n",
163
- " <th>seq</th>\n",
164
- " <th>smiles</th>\n",
165
- " <th>affinity_uM</th>\n",
166
- " </tr>\n",
167
- " </thead>\n",
168
- " <tbody>\n",
169
- " <tr>\n",
170
- " <th>0</th>\n",
171
- " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
172
- " <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
173
- " <td>0.00024</td>\n",
174
- " </tr>\n",
175
- " <tr>\n",
176
- " <th>1</th>\n",
177
- " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
178
- " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn...</td>\n",
179
- " <td>0.00025</td>\n",
180
- " </tr>\n",
181
- " <tr>\n",
182
- " <th>2</th>\n",
183
- " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
184
- " <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=...</td>\n",
185
- " <td>0.00041</td>\n",
186
- " </tr>\n",
187
- " <tr>\n",
188
- " <th>3</th>\n",
189
- " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
190
- " <td>OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@...</td>\n",
191
- " <td>0.00080</td>\n",
192
- " </tr>\n",
193
- " <tr>\n",
194
- " <th>4</th>\n",
195
- " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
196
- " <td>OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H...</td>\n",
197
- " <td>0.00099</td>\n",
198
- " </tr>\n",
199
- " <tr>\n",
200
- " <th>...</th>\n",
201
- " <td>...</td>\n",
202
- " <td>...</td>\n",
203
- " <td>...</td>\n",
204
- " </tr>\n",
205
- " <tr>\n",
206
- " <th>4453</th>\n",
207
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
208
- " <td>CC(C)C[C@H](NC(=O)N1CCC(CC1)C(=O)Nc1ccc(cc1)-c...</td>\n",
209
- " <td>0.00940</td>\n",
210
- " </tr>\n",
211
- " <tr>\n",
212
- " <th>4454</th>\n",
213
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
214
- " <td>CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cncc...</td>\n",
215
- " <td>0.01100</td>\n",
216
- " </tr>\n",
217
- " <tr>\n",
218
- " <th>4455</th>\n",
219
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
220
- " <td>CC(C)C[C@H](NC(=O)N1CCCC(C1)C(=O)Nc1cnccn1)C(=...</td>\n",
221
- " <td>0.35500</td>\n",
222
- " </tr>\n",
223
- " <tr>\n",
224
- " <th>4456</th>\n",
225
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
226
- " <td>COc1ccc(NC(=O)N2CCC(CC2)C(=O)N[C@@H](CC(C)C)C(...</td>\n",
227
- " <td>0.01700</td>\n",
228
- " </tr>\n",
229
- " <tr>\n",
230
- " <th>4457</th>\n",
231
- " <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
232
- " <td>CC(C)C[C@H](NC(=O)C1CCN(CC1)C(=O)Nc1cnccn1)C(=...</td>\n",
233
- " <td>0.07600</td>\n",
234
- " </tr>\n",
235
- " </tbody>\n",
236
- "</table>\n",
237
- "<p>2389700 rows × 3 columns</p>\n",
238
- "</div>"
239
- ],
240
- "text/plain": [
241
- " seq \\\n",
242
- "0 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
243
- "1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
244
- "2 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
245
- "3 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
246
- "4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
247
- "... ... \n",
248
- "4453 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... \n",
249
- "4454 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... \n",
250
- "4455 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... \n",
251
- "4456 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... \n",
252
- "4457 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... \n",
253
- "\n",
254
- " smiles affinity_uM \n",
255
- "0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 0.00024 \n",
256
- "1 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn... 0.00025 \n",
257
- "2 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=... 0.00041 \n",
258
- "3 OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@... 0.00080 \n",
259
- "4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... 0.00099 \n",
260
- "... ... ... \n",
261
- "4453 CC(C)C[C@H](NC(=O)N1CCC(CC1)C(=O)Nc1ccc(cc1)-c... 0.00940 \n",
262
- "4454 CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cncc... 0.01100 \n",
263
- "4455 CC(C)C[C@H](NC(=O)N1CCCC(C1)C(=O)Nc1cnccn1)C(=... 0.35500 \n",
264
- "4456 COc1ccc(NC(=O)N2CCC(CC2)C(=O)N[C@@H](CC(C)C)C(... 0.01700 \n",
265
- "4457 CC(C)C[C@H](NC(=O)C1CCN(CC1)C(=O)Nc1cnccn1)C(=... 0.07600 \n",
266
- "\n",
267
- "[2389700 rows x 3 columns]"
268
- ]
269
- },
270
- "execution_count": 120,
271
- "metadata": {},
272
- "output_type": "execute_result"
273
- }
274
- ],
275
- "source": [
276
- "df_bindingdb"
277
- ]
278
- },
279
- {
280
- "cell_type": "code",
281
- "execution_count": 88,
282
  "id": "d1abe1c8-ac66-4289-8964-367a5b18528d",
283
  "metadata": {},
284
  "outputs": [],
@@ -289,7 +146,7 @@
289
  },
290
  {
291
  "cell_type": "code",
292
- "execution_count": 89,
293
  "id": "988bab9c-5147-44e2-92ef-902eaf3c5a90",
294
  "metadata": {},
295
  "outputs": [
@@ -370,7 +227,7 @@
370
  "4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... 0.00099 "
371
  ]
372
  },
373
- "execution_count": 89,
374
  "metadata": {},
375
  "output_type": "execute_result"
376
  }
@@ -381,7 +238,7 @@
381
  },
382
  {
383
  "cell_type": "code",
384
- "execution_count": 93,
385
  "id": "d7bfee2a-c4e6-48c9-b0c6-52f6a69c7453",
386
  "metadata": {},
387
  "outputs": [],
@@ -392,7 +249,7 @@
392
  },
393
  {
394
  "cell_type": "code",
395
- "execution_count": 94,
396
  "id": "25553199-1715-40fb-9260-427bdd6c3706",
397
  "metadata": {},
398
  "outputs": [
@@ -430,25 +287,25 @@
430
  " <td>0.000620</td>\n",
431
  " </tr>\n",
432
  " <tr>\n",
433
- " <th>2</th>\n",
434
  " <td>NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE...</td>\n",
435
  " <td>CC(=O)NO</td>\n",
436
  " <td>2.600000</td>\n",
437
  " </tr>\n",
438
  " <tr>\n",
439
- " <th>7</th>\n",
440
- " <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
441
- " <td>C#CCCOP(=O)(O)OP(=O)(O)O</td>\n",
442
- " <td>0.580000</td>\n",
443
  " </tr>\n",
444
  " <tr>\n",
445
- " <th>16</th>\n",
446
- " <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
447
- " <td>C#CCOP(=O)(O)OP(=O)(O)O</td>\n",
448
- " <td>0.770000</td>\n",
449
  " </tr>\n",
450
  " <tr>\n",
451
- " <th>17</th>\n",
452
  " <td>MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV...</td>\n",
453
  " <td>c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3...</td>\n",
454
  " <td>15.000000</td>\n",
@@ -460,71 +317,71 @@
460
  " <td>...</td>\n",
461
  " </tr>\n",
462
  " <tr>\n",
463
- " <th>51900</th>\n",
464
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
465
  " <td>None</td>\n",
466
  " <td>127.226463</td>\n",
467
  " </tr>\n",
468
  " <tr>\n",
469
- " <th>51901</th>\n",
470
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
471
  " <td>None</td>\n",
472
  " <td>127.226463</td>\n",
473
  " </tr>\n",
474
  " <tr>\n",
475
- " <th>51902</th>\n",
476
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
477
  " <td>None</td>\n",
478
  " <td>169.204738</td>\n",
479
  " </tr>\n",
480
  " <tr>\n",
481
- " <th>51903</th>\n",
482
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
483
  " <td>None</td>\n",
484
  " <td>169.204738</td>\n",
485
  " </tr>\n",
486
  " <tr>\n",
487
- " <th>51904</th>\n",
488
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
489
  " <td>None</td>\n",
490
  " <td>169.204738</td>\n",
491
  " </tr>\n",
492
  " </tbody>\n",
493
  "</table>\n",
494
- "<p>25425 rows × 3 columns</p>\n",
495
  "</div>"
496
  ],
497
  "text/plain": [
498
  " seq \\\n",
499
  "0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
500
- "2 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
501
- "7 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
502
- "16 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
503
- "17 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
504
  "... ... \n",
505
- "51900 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
506
- "51901 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
507
- "51902 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
508
- "51903 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
509
- "51904 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
510
  "\n",
511
  " smiles affinity_uM \n",
512
  "0 NP(=O)(N)O 0.000620 \n",
513
- "2 CC(=O)NO 2.600000 \n",
514
- "7 C#CCCOP(=O)(O)OP(=O)(O)O 0.580000 \n",
515
- "16 C#CCOP(=O)(O)OP(=O)(O)O 0.770000 \n",
516
- "17 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... 15.000000 \n",
517
  "... ... ... \n",
518
- "51900 None 127.226463 \n",
519
- "51901 None 127.226463 \n",
520
- "51902 None 169.204738 \n",
521
- "51903 None 169.204738 \n",
522
- "51904 None 169.204738 \n",
523
  "\n",
524
- "[25425 rows x 3 columns]"
525
  ]
526
  },
527
- "execution_count": 94,
528
  "metadata": {},
529
  "output_type": "execute_result"
530
  }
@@ -535,7 +392,7 @@
535
  },
536
  {
537
  "cell_type": "code",
538
- "execution_count": 97,
539
  "id": "b2c936bc-cdc8-4bc1-b92d-f8755fd65f0a",
540
  "metadata": {},
541
  "outputs": [],
@@ -546,7 +403,7 @@
546
  },
547
  {
548
  "cell_type": "code",
549
- "execution_count": 98,
550
  "id": "cee93018-601d-458b-af44-bd978da7a2bc",
551
  "metadata": {},
552
  "outputs": [
@@ -581,31 +438,31 @@
581
  " <th>38</th>\n",
582
  " <td>PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...</td>\n",
583
  " <td>CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C</td>\n",
584
- " <td>1.500</td>\n",
585
  " </tr>\n",
586
  " <tr>\n",
587
  " <th>43</th>\n",
588
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
589
  " <td>OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c...</td>\n",
590
- " <td>24.000</td>\n",
591
  " </tr>\n",
592
  " <tr>\n",
593
  " <th>53</th>\n",
594
  " <td>EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKV...</td>\n",
595
  " <td>O[C@@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(C(CCCC(P(...</td>\n",
596
- " <td>NaN</td>\n",
597
  " </tr>\n",
598
  " <tr>\n",
599
  " <th>54</th>\n",
600
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
601
  " <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",
602
- " <td>10.000</td>\n",
603
  " </tr>\n",
604
  " <tr>\n",
605
  " <th>55</th>\n",
606
  " <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
607
  " <td>c1ccccc1</td>\n",
608
- " <td>175.000</td>\n",
609
  " </tr>\n",
610
  " <tr>\n",
611
  " <th>...</th>\n",
@@ -617,31 +474,31 @@
617
  " <th>105118</th>\n",
618
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
619
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
620
- " <td>NaN</td>\n",
621
  " </tr>\n",
622
  " <tr>\n",
623
  " <th>105119</th>\n",
624
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
625
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
626
- " <td>NaN</td>\n",
627
  " </tr>\n",
628
  " <tr>\n",
629
  " <th>105124</th>\n",
630
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
631
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
632
- " <td>125.000</td>\n",
633
  " </tr>\n",
634
  " <tr>\n",
635
  " <th>105133</th>\n",
636
  " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
637
  " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
638
- " <td>NaN</td>\n",
639
  " </tr>\n",
640
  " <tr>\n",
641
  " <th>105138</th>\n",
642
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
643
  " <td>CC[Se]C(=N)N</td>\n",
644
- " <td>0.039</td>\n",
645
  " </tr>\n",
646
  " </tbody>\n",
647
  "</table>\n",
@@ -663,22 +520,22 @@
663
  "105138 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
664
  "\n",
665
  " smiles affinity_uM \n",
666
- "38 CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C 1.500 \n",
667
- "43 OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c... 24.000 \n",
668
- "53 O[C@@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(C(CCCC(P(... NaN \n",
669
- "54 CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(... 10.000 \n",
670
- "55 c1ccccc1 175.000 \n",
671
  "... ... ... \n",
672
- "105118 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... NaN \n",
673
- "105119 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... NaN \n",
674
- "105124 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.000 \n",
675
- "105133 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... NaN \n",
676
- "105138 CC[Se]C(=N)N 0.039 \n",
677
  "\n",
678
  "[13645 rows x 3 columns]"
679
  ]
680
  },
681
- "execution_count": 98,
682
  "metadata": {},
683
  "output_type": "execute_result"
684
  }
@@ -689,7 +546,7 @@
689
  },
690
  {
691
  "cell_type": "code",
692
- "execution_count": 134,
693
  "id": "195f92db-fe06-4d03-8500-8d6c310a3347",
694
  "metadata": {},
695
  "outputs": [],
@@ -699,17 +556,17 @@
699
  },
700
  {
701
  "cell_type": "code",
702
- "execution_count": 135,
703
  "id": "d25c1e24-6566-4944-a0b4-944b3c8dbc6f",
704
  "metadata": {},
705
  "outputs": [
706
  {
707
  "data": {
708
  "text/plain": [
709
- "2446422"
710
  ]
711
  },
712
- "execution_count": 135,
713
  "metadata": {},
714
  "output_type": "execute_result"
715
  }
@@ -720,7 +577,7 @@
720
  },
721
  {
722
  "cell_type": "code",
723
- "execution_count": 105,
724
  "id": "c8287da2-cfdf-4d89-b175-f4c6b38ff8ac",
725
  "metadata": {},
726
  "outputs": [
@@ -750,7 +607,7 @@
750
  },
751
  {
752
  "cell_type": "code",
753
- "execution_count": 108,
754
  "id": "59a6706d-dab9-4ee0-8ef6-33537a3622a4",
755
  "metadata": {},
756
  "outputs": [],
@@ -760,7 +617,7 @@
760
  },
761
  {
762
  "cell_type": "code",
763
- "execution_count": 5,
764
  "id": "4ccf2ee5-d369-4c0e-bb91-792765d661bf",
765
  "metadata": {},
766
  "outputs": [],
@@ -770,7 +627,7 @@
770
  },
771
  {
772
  "cell_type": "code",
773
- "execution_count": 14,
774
  "id": "8a4bbb18-e62f-4774-ac6b-8a1be68204c1",
775
  "metadata": {},
776
  "outputs": [],
@@ -781,17 +638,17 @@
781
  },
782
  {
783
  "cell_type": "code",
784
- "execution_count": 15,
785
  "id": "d210fe56-a7eb-4adc-a77a-14c0c6d0034e",
786
  "metadata": {},
787
  "outputs": [
788
  {
789
  "data": {
790
  "text/plain": [
791
- "2430135"
792
  ]
793
  },
794
- "execution_count": 15,
795
  "metadata": {},
796
  "output_type": "execute_result"
797
  }
@@ -802,7 +659,7 @@
802
  },
803
  {
804
  "cell_type": "code",
805
- "execution_count": 16,
806
  "id": "d12b365d-98bd-4b61-b836-1a08d2e55418",
807
  "metadata": {},
808
  "outputs": [],
@@ -813,7 +670,7 @@
813
  },
814
  {
815
  "cell_type": "code",
816
- "execution_count": 17,
817
  "id": "80c15210-1af3-436e-970b-f81fc596fb41",
818
  "metadata": {},
819
  "outputs": [],
@@ -823,7 +680,7 @@
823
  },
824
  {
825
  "cell_type": "code",
826
- "execution_count": 18,
827
  "id": "30c314b8-8fe7-48ae-a2b8-149de1471b0c",
828
  "metadata": {},
829
  "outputs": [
@@ -839,7 +696,7 @@
839
  "dtype: object"
840
  ]
841
  },
842
- "execution_count": 18,
843
  "metadata": {},
844
  "output_type": "execute_result"
845
  }
@@ -850,7 +707,7 @@
850
  },
851
  {
852
  "cell_type": "code",
853
- "execution_count": 19,
854
  "id": "70a0a820-4d0c-4472-af96-9c301c0ab204",
855
  "metadata": {},
856
  "outputs": [],
@@ -860,7 +717,7 @@
860
  },
861
  {
862
  "cell_type": "code",
863
- "execution_count": 21,
864
  "id": "13d092fa-5625-40d0-b7ec-e3405ea20279",
865
  "metadata": {},
866
  "outputs": [
@@ -899,45 +756,9 @@
899
  " <tbody>\n",
900
  " <tr>\n",
901
  " <th>0</th>\n",
902
- " <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
903
- " <td>OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...</td>\n",
904
- " <td>500.000</td>\n",
905
- " <td>2147483648</td>\n",
906
- " <td>3242590208</td>\n",
907
- " <td>1914732547</td>\n",
908
- " <td>994116706</td>\n",
909
- " <td>3748288829</td>\n",
910
- " <td>124</td>\n",
911
- " </tr>\n",
912
- " <tr>\n",
913
- " <th>1</th>\n",
914
- " <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
915
- " <td>COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...</td>\n",
916
- " <td>0.023</td>\n",
917
- " <td>131072</td>\n",
918
- " <td>1109655552</td>\n",
919
- " <td>2123376961</td>\n",
920
- " <td>3477340882</td>\n",
921
- " <td>2951175957</td>\n",
922
- " <td>252</td>\n",
923
- " </tr>\n",
924
- " <tr>\n",
925
- " <th>2</th>\n",
926
- " <td>GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPA...</td>\n",
927
- " <td>O[C@H]1O[C@H](CO[P](=O)(=O)=O)[C@H]([C@H]([C@H...</td>\n",
928
- " <td>6300.000</td>\n",
929
- " <td>67108864</td>\n",
930
- " <td>1082523648</td>\n",
931
- " <td>1879080960</td>\n",
932
- " <td>461382690</td>\n",
933
- " <td>3576355128</td>\n",
934
- " <td>28</td>\n",
935
- " </tr>\n",
936
- " <tr>\n",
937
- " <th>3</th>\n",
938
  " <td>SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP...</td>\n",
939
  " <td>OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(...</td>\n",
940
- " <td>0.210</td>\n",
941
  " <td>2147484672</td>\n",
942
  " <td>36176898</td>\n",
943
  " <td>850664773</td>\n",
@@ -946,10 +767,10 @@
946
  " <td>252</td>\n",
947
  " </tr>\n",
948
  " <tr>\n",
949
- " <th>4</th>\n",
950
  " <td>EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI...</td>\n",
951
  " <td>O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2...</td>\n",
952
- " <td>0.050</td>\n",
953
  " <td>0</td>\n",
954
  " <td>1858306115</td>\n",
955
  " <td>4223456596</td>\n",
@@ -958,6 +779,42 @@
958
  " <td>124</td>\n",
959
  " </tr>\n",
960
  " <tr>\n",
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
961
  " <th>...</th>\n",
962
  " <td>...</td>\n",
963
  " <td>...</td>\n",
@@ -970,46 +827,34 @@
970
  " <td>...</td>\n",
971
  " </tr>\n",
972
  " <tr>\n",
973
- " <th>2430130</th>\n",
974
- " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
975
- " <td>O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(...</td>\n",
976
- " <td>8.000</td>\n",
977
- " <td>0</td>\n",
978
- " <td>612865025</td>\n",
979
- " <td>3107729684</td>\n",
980
- " <td>2146870234</td>\n",
981
- " <td>4286578680</td>\n",
982
  " <td>252</td>\n",
983
  " </tr>\n",
984
  " <tr>\n",
985
- " <th>2430131</th>\n",
986
- " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
987
- " <td>CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H...</td>\n",
988
- " <td>8.000</td>\n",
989
- " <td>0</td>\n",
990
- " <td>136194</td>\n",
991
- " <td>1025390336</td>\n",
992
- " <td>1612680088</td>\n",
993
- " <td>2071973584</td>\n",
994
  " <td>252</td>\n",
995
  " </tr>\n",
996
  " <tr>\n",
997
- " <th>2430132</th>\n",
998
- " <td>RWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVS...</td>\n",
999
- " <td>ONC(=O)CC1(CCOCC1)S(=O)(=O)c1ccc(cc1)Oc1ccccc1</td>\n",
1000
- " <td>0.023</td>\n",
1001
- " <td>2147483648</td>\n",
1002
- " <td>2081488896</td>\n",
1003
- " <td>3124936893</td>\n",
1004
- " <td>264668962</td>\n",
1005
- " <td>4286183928</td>\n",
1006
- " <td>124</td>\n",
1007
- " </tr>\n",
1008
- " <tr>\n",
1009
- " <th>2430133</th>\n",
1010
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
1011
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
1012
- " <td>125.000</td>\n",
1013
  " <td>67108864</td>\n",
1014
  " <td>1115688962</td>\n",
1015
  " <td>1771869508</td>\n",
@@ -1018,10 +863,22 @@
1018
  " <td>124</td>\n",
1019
  " </tr>\n",
1020
  " <tr>\n",
1021
- " <th>2430134</th>\n",
 
 
 
 
 
 
 
 
 
 
 
 
1022
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
1023
  " <td>CC[Se]C(=N)N</td>\n",
1024
- " <td>0.039</td>\n",
1025
  " <td>16</td>\n",
1026
  " <td>6144</td>\n",
1027
  " <td>537396736</td>\n",
@@ -1031,53 +888,53 @@
1031
  " </tr>\n",
1032
  " </tbody>\n",
1033
  "</table>\n",
1034
- "<p>2430135 rows × 9 columns</p>\n",
1035
  "</div>"
1036
  ],
1037
  "text/plain": [
1038
- " seq \\\n",
1039
- "0 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n",
1040
- "1 VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n",
1041
- "2 GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPA... \n",
1042
- "3 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP... \n",
1043
- "4 EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI... \n",
1044
- "... ... \n",
1045
- "2430130 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
1046
- "2430131 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
1047
- "2430132 RWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVS... \n",
1048
- "2430133 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
1049
- "2430134 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
1050
  "\n",
1051
- " smiles affinity_uM \\\n",
1052
- "0 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.000 \n",
1053
- "1 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.023 \n",
1054
- "2 O[C@H]1O[C@H](CO[P](=O)(=O)=O)[C@H]([C@H]([C@H... 6300.000 \n",
1055
- "3 OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(... 0.210 \n",
1056
- "4 O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2... 0.050 \n",
1057
- "... ... ... \n",
1058
- "2430130 O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(... 8.000 \n",
1059
- "2430131 CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H... 8.000 \n",
1060
- "2430132 ONC(=O)CC1(CCOCC1)S(=O)(=O)c1ccc(cc1)Oc1ccccc1 0.023 \n",
1061
- "2430133 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.000 \n",
1062
- "2430134 CC[Se]C(=N)N 0.039 \n",
1063
  "\n",
1064
- " 0 1 2 3 4 5 \n",
1065
- "0 2147483648 3242590208 1914732547 994116706 3748288829 124 \n",
1066
- "1 131072 1109655552 2123376961 3477340882 2951175957 252 \n",
1067
- "2 67108864 1082523648 1879080960 461382690 3576355128 28 \n",
1068
- "3 2147484672 36176898 850664773 3978479102 1599828989 252 \n",
1069
- "4 0 1858306115 4223456596 4018595822 4282121085 124 \n",
1070
- "... ... ... ... ... ... ... \n",
1071
- "2430130 0 612865025 3107729684 2146870234 4286578680 252 \n",
1072
- "2430131 0 136194 1025390336 1612680088 2071973584 252 \n",
1073
- "2430132 2147483648 2081488896 3124936893 264668962 4286183928 124 \n",
1074
- "2430133 67108864 1115688962 1771869508 4018431718 3744193341 124 \n",
1075
- "2430134 16 6144 537396736 2170880 1510015504 192 \n",
1076
  "\n",
1077
- "[2430135 rows x 9 columns]"
1078
  ]
1079
  },
1080
- "execution_count": 21,
1081
  "metadata": {},
1082
  "output_type": "execute_result"
1083
  }
@@ -1088,7 +945,7 @@
1088
  },
1089
  {
1090
  "cell_type": "code",
1091
- "execution_count": 22,
1092
  "id": "30f7fff7-3cfe-41c8-97c9-666f3e256222",
1093
  "metadata": {},
1094
  "outputs": [
@@ -1098,7 +955,7 @@
1098
  "Index(['seq', 'smiles', 'affinity_uM', 0, 1, 2, 3, 4, 5], dtype='object')"
1099
  ]
1100
  },
1101
- "execution_count": 22,
1102
  "metadata": {},
1103
  "output_type": "execute_result"
1104
  }
@@ -1109,7 +966,7 @@
1109
  },
1110
  {
1111
  "cell_type": "code",
1112
- "execution_count": 23,
1113
  "id": "16d2b26e-984f-4c71-af19-a3e711ed9ca2",
1114
  "metadata": {},
1115
  "outputs": [],
@@ -1119,7 +976,7 @@
1119
  },
1120
  {
1121
  "cell_type": "code",
1122
- "execution_count": 24,
1123
  "id": "27fa2150-8152-444b-ba5b-24bea39fc098",
1124
  "metadata": {},
1125
  "outputs": [
@@ -1129,7 +986,7 @@
1129
  "Index(['smiles', 'affinity_uM'], dtype='object')"
1130
  ]
1131
  },
1132
- "execution_count": 24,
1133
  "metadata": {},
1134
  "output_type": "execute_result"
1135
  }
@@ -1140,7 +997,7 @@
1140
  },
1141
  {
1142
  "cell_type": "code",
1143
- "execution_count": 67,
1144
  "id": "89edacbc-52f3-4a76-90b0-95273f5e53b3",
1145
  "metadata": {},
1146
  "outputs": [],
@@ -1161,7 +1018,7 @@
1161
  },
1162
  {
1163
  "cell_type": "code",
1164
- "execution_count": 69,
1165
  "id": "0cad3882-975d-4693-aad1-63ec26646bd0",
1166
  "metadata": {},
1167
  "outputs": [
@@ -1180,7 +1037,7 @@
1180
  },
1181
  {
1182
  "cell_type": "code",
1183
- "execution_count": 70,
1184
  "id": "c200e29a-3f14-41f4-b620-ccce0eb0d5ce",
1185
  "metadata": {},
1186
  "outputs": [
@@ -1214,38 +1071,38 @@
1214
  " <tbody>\n",
1215
  " <tr>\n",
1216
  " <th>0</th>\n",
1217
- " <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
1218
- " <td>OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...</td>\n",
1219
- " <td>500.000</td>\n",
1220
- " <td>3.301030</td>\n",
1221
  " </tr>\n",
1222
  " <tr>\n",
1223
  " <th>1</th>\n",
1224
- " <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
1225
- " <td>COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...</td>\n",
1226
- " <td>0.023</td>\n",
1227
- " <td>7.638272</td>\n",
1228
  " </tr>\n",
1229
  " <tr>\n",
1230
  " <th>2</th>\n",
1231
- " <td>GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPA...</td>\n",
1232
- " <td>O[C@H]1O[C@H](CO[P](=O)(=O)=O)[C@H]([C@H]([C@H...</td>\n",
1233
- " <td>6300.000</td>\n",
1234
- " <td>2.200659</td>\n",
1235
  " </tr>\n",
1236
  " <tr>\n",
1237
  " <th>3</th>\n",
1238
- " <td>SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP...</td>\n",
1239
- " <td>OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(...</td>\n",
1240
- " <td>0.210</td>\n",
1241
- " <td>6.677781</td>\n",
1242
  " </tr>\n",
1243
  " <tr>\n",
1244
  " <th>4</th>\n",
1245
- " <td>EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI...</td>\n",
1246
- " <td>O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2...</td>\n",
1247
- " <td>0.050</td>\n",
1248
- " <td>7.301030</td>\n",
1249
  " </tr>\n",
1250
  " <tr>\n",
1251
  " <th>...</th>\n",
@@ -1255,89 +1112,89 @@
1255
  " <td>...</td>\n",
1256
  " </tr>\n",
1257
  " <tr>\n",
1258
- " <th>1849400</th>\n",
1259
- " <td>KQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALA...</td>\n",
1260
- " <td>O[C@@H]1[C@H](O)[C@H](O[C@H]1n1cnc2c1ncnc2N)CO...</td>\n",
1261
- " <td>250.000</td>\n",
1262
- " <td>3.602060</td>\n",
1263
- " </tr>\n",
1264
- " <tr>\n",
1265
- " <th>1849401</th>\n",
1266
  " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
1267
- " <td>O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(...</td>\n",
1268
- " <td>8.000</td>\n",
1269
  " <td>5.096910</td>\n",
1270
  " </tr>\n",
1271
  " <tr>\n",
1272
- " <th>1849402</th>\n",
1273
- " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
1274
- " <td>CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H...</td>\n",
1275
- " <td>8.000</td>\n",
1276
- " <td>5.096910</td>\n",
1277
  " </tr>\n",
1278
  " <tr>\n",
1279
- " <th>1849403</th>\n",
1280
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
1281
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
1282
- " <td>125.000</td>\n",
1283
  " <td>3.903090</td>\n",
1284
  " </tr>\n",
1285
  " <tr>\n",
1286
- " <th>1849404</th>\n",
 
 
 
 
 
 
 
1287
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
1288
  " <td>CC[Se]C(=N)N</td>\n",
1289
- " <td>0.039</td>\n",
1290
  " <td>7.408935</td>\n",
1291
  " </tr>\n",
1292
  " </tbody>\n",
1293
  "</table>\n",
1294
- "<p>1849405 rows × 4 columns</p>\n",
1295
  "</div>"
1296
  ],
1297
  "text/plain": [
1298
- " seq \\\n",
1299
- "0 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n",
1300
- "1 VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n",
1301
- "2 GMRVYLGADHAGYELKQRIIEHLKQTGHEPIDCGALRYDADDDYPA... \n",
1302
- "3 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP... \n",
1303
- "4 EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI... \n",
1304
- "... ... \n",
1305
- "1849400 KQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALA... \n",
1306
- "1849401 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
1307
- "1849402 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
1308
- "1849403 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
1309
- "1849404 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
1310
  "\n",
1311
- " smiles affinity_uM \\\n",
1312
- "0 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.000 \n",
1313
- "1 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.023 \n",
1314
- "2 O[C@H]1O[C@H](CO[P](=O)(=O)=O)[C@H]([C@H]([C@H... 6300.000 \n",
1315
- "3 OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(... 0.210 \n",
1316
- "4 O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2... 0.050 \n",
1317
- "... ... ... \n",
1318
- "1849400 O[C@@H]1[C@H](O)[C@H](O[C@H]1n1cnc2c1ncnc2N)CO... 250.000 \n",
1319
- "1849401 O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(... 8.000 \n",
1320
- "1849402 CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H... 8.000 \n",
1321
- "1849403 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.000 \n",
1322
- "1849404 CC[Se]C(=N)N 0.039 \n",
1323
  "\n",
1324
- " neg_log10_affinity_M \n",
1325
- "0 3.301030 \n",
1326
- "1 7.638272 \n",
1327
- "2 2.200659 \n",
1328
- "3 6.677781 \n",
1329
- "4 7.301030 \n",
1330
- "... ... \n",
1331
- "1849400 3.602060 \n",
1332
- "1849401 5.096910 \n",
1333
- "1849402 5.096910 \n",
1334
- "1849403 3.903090 \n",
1335
- "1849404 7.408935 \n",
1336
  "\n",
1337
- "[1849405 rows x 4 columns]"
1338
  ]
1339
  },
1340
- "execution_count": 70,
1341
  "metadata": {},
1342
  "output_type": "execute_result"
1343
  }
@@ -1348,7 +1205,7 @@
1348
  },
1349
  {
1350
  "cell_type": "code",
1351
- "execution_count": 72,
1352
  "id": "7f4027a2-0a5f-47bf-8a34-0c6a73b9b112",
1353
  "metadata": {},
1354
  "outputs": [],
@@ -1358,27 +1215,7 @@
1358
  },
1359
  {
1360
  "cell_type": "code",
1361
- "execution_count": 86,
1362
- "id": "c558f3f6-9fe7-4361-8272-23a54368fdda",
1363
- "metadata": {},
1364
- "outputs": [],
1365
- "source": [
1366
- "df.to_parquet('data/all_nocan.parquet')"
1367
- ]
1368
- },
1369
- {
1370
- "cell_type": "code",
1371
- "execution_count": 11,
1372
- "id": "4e2d89f7-f6ea-41de-a13b-4a184b4fd580",
1373
- "metadata": {},
1374
- "outputs": [],
1375
- "source": [
1376
- "df = pd.read_parquet('data/all_nocan.parquet')"
1377
- ]
1378
- },
1379
- {
1380
- "cell_type": "code",
1381
- "execution_count": 5,
1382
  "id": "b4b9acd7-7784-492b-9fa3-b7fad9d18a9d",
1383
  "metadata": {},
1384
  "outputs": [
@@ -1386,7 +1223,7 @@
1386
  "name": "stdout",
1387
  "output_type": "stream",
1388
  "text": [
1389
- "INFO: Pandarallel will run on 256 workers.\n",
1390
  "INFO: Pandarallel will use Memory file system to transfer data between the main process and workers.\n"
1391
  ]
1392
  }
@@ -1398,7 +1235,7 @@
1398
  },
1399
  {
1400
  "cell_type": "code",
1401
- "execution_count": 12,
1402
  "id": "eb99774f-9bcc-454d-b5e5-a8470223d6ca",
1403
  "metadata": {},
1404
  "outputs": [],
@@ -1413,17 +1250,30 @@
1413
  },
1414
  {
1415
  "cell_type": "code",
1416
- "execution_count": 14,
1417
  "id": "4d44bd8e-f2e1-44b4-aea7-40b4437baf44",
1418
  "metadata": {},
1419
- "outputs": [],
 
 
 
 
 
 
 
 
 
 
 
 
 
1420
  "source": [
1421
  "df['smiles_can'] = df['smiles'].parallel_apply(make_canonical)"
1422
  ]
1423
  },
1424
  {
1425
  "cell_type": "code",
1426
- "execution_count": 8,
1427
  "id": "07ffdeb1-f4fa-4776-9fea-a18439e03d2e",
1428
  "metadata": {},
1429
  "outputs": [],
@@ -1433,7 +1283,7 @@
1433
  },
1434
  {
1435
  "cell_type": "code",
1436
- "execution_count": 4,
1437
  "id": "8f949038-d07d-4d3a-a47e-b825cc9018ca",
1438
  "metadata": {},
1439
  "outputs": [],
@@ -1443,7 +1293,7 @@
1443
  },
1444
  {
1445
  "cell_type": "code",
1446
- "execution_count": 5,
1447
  "id": "0c027988-0b44-4010-ad61-7d70eead1654",
1448
  "metadata": {},
1449
  "outputs": [],
@@ -1453,7 +1303,7 @@
1453
  },
1454
  {
1455
  "cell_type": "code",
1456
- "execution_count": 33,
1457
  "id": "6aeba020-b6ff-4633-902e-4df74463eb2f",
1458
  "metadata": {},
1459
  "outputs": [],
@@ -1463,17 +1313,17 @@
1463
  },
1464
  {
1465
  "cell_type": "code",
1466
- "execution_count": 31,
1467
  "id": "91196eee-5fd0-4aa4-927a-5c1a3f436ac8",
1468
  "metadata": {},
1469
  "outputs": [
1470
  {
1471
  "data": {
1472
  "text/plain": [
1473
- "(array([6.49685099]), array([2.43570803]))"
1474
  ]
1475
  },
1476
- "execution_count": 31,
1477
  "metadata": {},
1478
  "output_type": "execute_result"
1479
  }
@@ -1484,17 +1334,17 @@
1484
  },
1485
  {
1486
  "cell_type": "code",
1487
- "execution_count": 24,
1488
- "id": "9be91c11-1c58-47de-8ebb-99c25cfc3c55",
1489
  "metadata": {},
1490
  "outputs": [],
1491
  "source": [
1492
- "df = df.drop(columns=['level_0','index'])"
1493
  ]
1494
  },
1495
  {
1496
  "cell_type": "code",
1497
- "execution_count": 16,
1498
  "id": "c6c64066-4032-4247-a8b9-00388176cc7b",
1499
  "metadata": {},
1500
  "outputs": [],
@@ -1504,19 +1354,19 @@
1504
  },
1505
  {
1506
  "cell_type": "code",
1507
- "execution_count": 18,
1508
  "id": "469cf0dd-7b87-4245-973c-2a445e1fcca9",
1509
  "metadata": {},
1510
  "outputs": [
1511
  {
1512
  "data": {
1513
  "text/plain": [
1514
- "Index(['seq', 'smiles', 'affinity_uM', 'neg_log10_affinity_M', 'affinity',\n",
1515
- " 'smiles_can'],\n",
1516
  " dtype='object')"
1517
  ]
1518
  },
1519
- "execution_count": 18,
1520
  "metadata": {},
1521
  "output_type": "execute_result"
1522
  }
@@ -1527,13 +1377,13 @@
1527
  },
1528
  {
1529
  "cell_type": "code",
1530
- "execution_count": 19,
1531
  "id": "d91c0d91-474c-4ab2-9a5e-3b7861f7a832",
1532
  "metadata": {},
1533
  "outputs": [
1534
  {
1535
  "data": {
1536
- "image/png": "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\n",
1537
  "text/plain": [
1538
  "<Figure size 432x288 with 1 Axes>"
1539
  ]
@@ -1553,50 +1403,29 @@
1553
  },
1554
  {
1555
  "cell_type": "code",
1556
- "execution_count": 6,
1557
- "id": "9ca8df46-15d3-40f9-b304-dd6e5597be5e",
1558
- "metadata": {},
1559
- "outputs": [
1560
- {
1561
- "data": {
1562
- "text/plain": [
1563
- "0.17005836848632214"
1564
- ]
1565
- },
1566
- "execution_count": 6,
1567
- "metadata": {},
1568
- "output_type": "execute_result"
1569
- }
1570
- ],
1571
- "source": [
1572
- "(df['neg_log10_affinity_M']<5).sum()/len(df)"
1573
- ]
1574
- },
1575
- {
1576
- "cell_type": "code",
1577
- "execution_count": 1,
1578
- "id": "88cf855d-704f-4ed4-827e-9f4e3288b3a0",
1579
  "metadata": {},
1580
  "outputs": [
1581
  {
1582
  "data": {
1583
  "text/plain": [
1584
- "0.001298888888888889"
1585
  ]
1586
  },
1587
- "execution_count": 1,
1588
  "metadata": {},
1589
  "output_type": "execute_result"
1590
  }
1591
  ],
1592
  "source": [
1593
- "2338/1.8e6"
1594
  ]
1595
  },
1596
  {
1597
  "cell_type": "code",
1598
  "execution_count": null,
1599
- "id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
1600
  "metadata": {},
1601
  "outputs": [],
1602
  "source": []
@@ -1618,7 +1447,7 @@
1618
  "name": "python",
1619
  "nbconvert_exporter": "python",
1620
  "pygments_lexer": "ipython3",
1621
- "version": "3.8.10"
1622
  }
1623
  },
1624
  "nbformat": 4,
 
12
  },
13
  {
14
  "cell_type": "code",
15
+ "execution_count": 2,
16
  "id": "b0859483-5e19-4280-9f53-0d00a6f22d34",
17
  "metadata": {},
18
  "outputs": [],
 
23
  },
24
  {
25
  "cell_type": "code",
26
+ "execution_count": 3,
27
  "id": "f30732b7-7444-47ad-84e7-566e7a6f2f8e",
28
  "metadata": {},
29
  "outputs": [
 
62
  " </tr>\n",
63
  " <tr>\n",
64
  " <th>1</th>\n",
65
+ " <td>AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...</td>\n",
66
+ " <td>OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)[C-](=O)=O)NC...</td>\n",
67
+ " <td>6.430</td>\n",
68
  " </tr>\n",
69
  " <tr>\n",
70
  " <th>2</th>\n",
71
+ " <td>PFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNL...</td>\n",
72
+ " <td>CC[C@@H]([C@@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H]...</td>\n",
73
+ " <td>190.000</td>\n",
74
  " </tr>\n",
75
  " <tr>\n",
76
  " <th>3</th>\n",
77
+ " <td>SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP...</td>\n",
78
+ " <td>OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(...</td>\n",
79
+ " <td>0.210</td>\n",
80
  " </tr>\n",
81
  " <tr>\n",
82
  " <th>4</th>\n",
83
+ " <td>EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI...</td>\n",
84
+ " <td>O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2...</td>\n",
85
+ " <td>0.050</td>\n",
86
  " </tr>\n",
87
  " </tbody>\n",
88
  "</table>\n",
 
91
  "text/plain": [
92
  " seq \\\n",
93
  "0 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",
94
+ "1 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
95
+ "2 PFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNL... \n",
96
+ "3 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP... \n",
97
+ "4 EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI... \n",
98
  "\n",
99
  " smiles affinity_uM \n",
100
  "0 CCCCCCCCCCCCCCCCCCC[C-](=O)=O 0.026 \n",
101
+ "1 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)[C-](=O)=O)NC... 6.430 \n",
102
+ "2 CC[C@@H]([C@@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H]... 190.000 \n",
103
+ "3 OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(... 0.210 \n",
104
+ "4 O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2... 0.050 "
105
  ]
106
  },
107
+ "execution_count": 3,
108
  "metadata": {},
109
  "output_type": "execute_result"
110
  }
 
115
  },
116
  {
117
  "cell_type": "code",
118
+ "execution_count": 4,
119
  "id": "2787b9fd-3d6f-4ae3-a3ad-d3539b72782b",
120
  "metadata": {},
121
  "outputs": [],
 
135
  },
136
  {
137
  "cell_type": "code",
138
+ "execution_count": 6,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
139
  "id": "d1abe1c8-ac66-4289-8964-367a5b18528d",
140
  "metadata": {},
141
  "outputs": [],
 
146
  },
147
  {
148
  "cell_type": "code",
149
+ "execution_count": 7,
150
  "id": "988bab9c-5147-44e2-92ef-902eaf3c5a90",
151
  "metadata": {},
152
  "outputs": [
 
227
  "4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... 0.00099 "
228
  ]
229
  },
230
+ "execution_count": 7,
231
  "metadata": {},
232
  "output_type": "execute_result"
233
  }
 
238
  },
239
  {
240
  "cell_type": "code",
241
+ "execution_count": 8,
242
  "id": "d7bfee2a-c4e6-48c9-b0c6-52f6a69c7453",
243
  "metadata": {},
244
  "outputs": [],
 
249
  },
250
  {
251
  "cell_type": "code",
252
+ "execution_count": 9,
253
  "id": "25553199-1715-40fb-9260-427bdd6c3706",
254
  "metadata": {},
255
  "outputs": [
 
287
  " <td>0.000620</td>\n",
288
  " </tr>\n",
289
  " <tr>\n",
290
+ " <th>1</th>\n",
291
  " <td>NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE...</td>\n",
292
  " <td>CC(=O)NO</td>\n",
293
  " <td>2.600000</td>\n",
294
  " </tr>\n",
295
  " <tr>\n",
296
+ " <th>2</th>\n",
297
+ " <td>MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV...</td>\n",
298
+ " <td>c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3...</td>\n",
299
+ " <td>15.000000</td>\n",
300
  " </tr>\n",
301
  " <tr>\n",
302
+ " <th>3</th>\n",
303
+ " <td>MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV...</td>\n",
304
+ " <td>c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3...</td>\n",
305
+ " <td>15.000000</td>\n",
306
  " </tr>\n",
307
  " <tr>\n",
308
+ " <th>4</th>\n",
309
  " <td>MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV...</td>\n",
310
  " <td>c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3...</td>\n",
311
  " <td>15.000000</td>\n",
 
317
  " <td>...</td>\n",
318
  " </tr>\n",
319
  " <tr>\n",
320
+ " <th>17682</th>\n",
321
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
322
  " <td>None</td>\n",
323
  " <td>127.226463</td>\n",
324
  " </tr>\n",
325
  " <tr>\n",
326
+ " <th>17683</th>\n",
327
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
328
  " <td>None</td>\n",
329
  " <td>127.226463</td>\n",
330
  " </tr>\n",
331
  " <tr>\n",
332
+ " <th>17684</th>\n",
333
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
334
  " <td>None</td>\n",
335
  " <td>169.204738</td>\n",
336
  " </tr>\n",
337
  " <tr>\n",
338
+ " <th>17685</th>\n",
339
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
340
  " <td>None</td>\n",
341
  " <td>169.204738</td>\n",
342
  " </tr>\n",
343
  " <tr>\n",
344
+ " <th>17686</th>\n",
345
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
346
  " <td>None</td>\n",
347
  " <td>169.204738</td>\n",
348
  " </tr>\n",
349
  " </tbody>\n",
350
  "</table>\n",
351
+ "<p>17687 rows × 3 columns</p>\n",
352
  "</div>"
353
  ],
354
  "text/plain": [
355
  " seq \\\n",
356
  "0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
357
+ "1 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
358
+ "2 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
359
+ "3 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
360
+ "4 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
361
  "... ... \n",
362
+ "17682 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
363
+ "17683 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
364
+ "17684 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
365
+ "17685 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
366
+ "17686 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
367
  "\n",
368
  " smiles affinity_uM \n",
369
  "0 NP(=O)(N)O 0.000620 \n",
370
+ "1 CC(=O)NO 2.600000 \n",
371
+ "2 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... 15.000000 \n",
372
+ "3 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... 15.000000 \n",
373
+ "4 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... 15.000000 \n",
374
  "... ... ... \n",
375
+ "17682 None 127.226463 \n",
376
+ "17683 None 127.226463 \n",
377
+ "17684 None 169.204738 \n",
378
+ "17685 None 169.204738 \n",
379
+ "17686 None 169.204738 \n",
380
  "\n",
381
+ "[17687 rows x 3 columns]"
382
  ]
383
  },
384
+ "execution_count": 9,
385
  "metadata": {},
386
  "output_type": "execute_result"
387
  }
 
392
  },
393
  {
394
  "cell_type": "code",
395
+ "execution_count": 10,
396
  "id": "b2c936bc-cdc8-4bc1-b92d-f8755fd65f0a",
397
  "metadata": {},
398
  "outputs": [],
 
403
  },
404
  {
405
  "cell_type": "code",
406
+ "execution_count": 11,
407
  "id": "cee93018-601d-458b-af44-bd978da7a2bc",
408
  "metadata": {},
409
  "outputs": [
 
438
  " <th>38</th>\n",
439
  " <td>PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...</td>\n",
440
  " <td>CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C</td>\n",
441
+ " <td>1.5000</td>\n",
442
  " </tr>\n",
443
  " <tr>\n",
444
  " <th>43</th>\n",
445
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
446
  " <td>OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c...</td>\n",
447
+ " <td>24.0000</td>\n",
448
  " </tr>\n",
449
  " <tr>\n",
450
  " <th>53</th>\n",
451
  " <td>EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKV...</td>\n",
452
  " <td>O[C@@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(C(CCCC(P(...</td>\n",
453
+ " <td>6.0000</td>\n",
454
  " </tr>\n",
455
  " <tr>\n",
456
  " <th>54</th>\n",
457
  " <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
458
  " <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",
459
+ " <td>10.0000</td>\n",
460
  " </tr>\n",
461
  " <tr>\n",
462
  " <th>55</th>\n",
463
  " <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
464
  " <td>c1ccccc1</td>\n",
465
+ " <td>175.0000</td>\n",
466
  " </tr>\n",
467
  " <tr>\n",
468
  " <th>...</th>\n",
 
474
  " <th>105118</th>\n",
475
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
476
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
477
+ " <td>0.0045</td>\n",
478
  " </tr>\n",
479
  " <tr>\n",
480
  " <th>105119</th>\n",
481
  " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
482
  " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
483
+ " <td>0.0045</td>\n",
484
  " </tr>\n",
485
  " <tr>\n",
486
  " <th>105124</th>\n",
487
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
488
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
489
+ " <td>125.0000</td>\n",
490
  " </tr>\n",
491
  " <tr>\n",
492
  " <th>105133</th>\n",
493
  " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
494
  " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
495
+ " <td>2.0000</td>\n",
496
  " </tr>\n",
497
  " <tr>\n",
498
  " <th>105138</th>\n",
499
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
500
  " <td>CC[Se]C(=N)N</td>\n",
501
+ " <td>0.0390</td>\n",
502
  " </tr>\n",
503
  " </tbody>\n",
504
  "</table>\n",
 
520
  "105138 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
521
  "\n",
522
  " smiles affinity_uM \n",
523
+ "38 CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C 1.5000 \n",
524
+ "43 OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c... 24.0000 \n",
525
+ "53 O[C@@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(C(CCCC(P(... 6.0000 \n",
526
+ "54 CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(... 10.0000 \n",
527
+ "55 c1ccccc1 175.0000 \n",
528
  "... ... ... \n",
529
+ "105118 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
530
+ "105119 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
531
+ "105124 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.0000 \n",
532
+ "105133 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
533
+ "105138 CC[Se]C(=N)N 0.0390 \n",
534
  "\n",
535
  "[13645 rows x 3 columns]"
536
  ]
537
  },
538
+ "execution_count": 11,
539
  "metadata": {},
540
  "output_type": "execute_result"
541
  }
 
546
  },
547
  {
548
  "cell_type": "code",
549
+ "execution_count": 12,
550
  "id": "195f92db-fe06-4d03-8500-8d6c310a3347",
551
  "metadata": {},
552
  "outputs": [],
 
556
  },
557
  {
558
  "cell_type": "code",
559
+ "execution_count": 13,
560
  "id": "d25c1e24-6566-4944-a0b4-944b3c8dbc6f",
561
  "metadata": {},
562
  "outputs": [
563
  {
564
  "data": {
565
  "text/plain": [
566
+ "674728"
567
  ]
568
  },
569
+ "execution_count": 13,
570
  "metadata": {},
571
  "output_type": "execute_result"
572
  }
 
577
  },
578
  {
579
  "cell_type": "code",
580
+ "execution_count": 14,
581
  "id": "c8287da2-cfdf-4d89-b175-f4c6b38ff8ac",
582
  "metadata": {},
583
  "outputs": [
 
607
  },
608
  {
609
  "cell_type": "code",
610
+ "execution_count": 16,
611
  "id": "59a6706d-dab9-4ee0-8ef6-33537a3622a4",
612
  "metadata": {},
613
  "outputs": [],
 
617
  },
618
  {
619
  "cell_type": "code",
620
+ "execution_count": 17,
621
  "id": "4ccf2ee5-d369-4c0e-bb91-792765d661bf",
622
  "metadata": {},
623
  "outputs": [],
 
627
  },
628
  {
629
  "cell_type": "code",
630
+ "execution_count": 18,
631
  "id": "8a4bbb18-e62f-4774-ac6b-8a1be68204c1",
632
  "metadata": {},
633
  "outputs": [],
 
638
  },
639
  {
640
  "cell_type": "code",
641
+ "execution_count": 19,
642
  "id": "d210fe56-a7eb-4adc-a77a-14c0c6d0034e",
643
  "metadata": {},
644
  "outputs": [
645
  {
646
  "data": {
647
  "text/plain": [
648
+ "662484"
649
  ]
650
  },
651
+ "execution_count": 19,
652
  "metadata": {},
653
  "output_type": "execute_result"
654
  }
 
659
  },
660
  {
661
  "cell_type": "code",
662
+ "execution_count": 20,
663
  "id": "d12b365d-98bd-4b61-b836-1a08d2e55418",
664
  "metadata": {},
665
  "outputs": [],
 
670
  },
671
  {
672
  "cell_type": "code",
673
+ "execution_count": 21,
674
  "id": "80c15210-1af3-436e-970b-f81fc596fb41",
675
  "metadata": {},
676
  "outputs": [],
 
680
  },
681
  {
682
  "cell_type": "code",
683
+ "execution_count": 22,
684
  "id": "30c314b8-8fe7-48ae-a2b8-149de1471b0c",
685
  "metadata": {},
686
  "outputs": [
 
696
  "dtype: object"
697
  ]
698
  },
699
+ "execution_count": 22,
700
  "metadata": {},
701
  "output_type": "execute_result"
702
  }
 
707
  },
708
  {
709
  "cell_type": "code",
710
+ "execution_count": 23,
711
  "id": "70a0a820-4d0c-4472-af96-9c301c0ab204",
712
  "metadata": {},
713
  "outputs": [],
 
717
  },
718
  {
719
  "cell_type": "code",
720
+ "execution_count": 24,
721
  "id": "13d092fa-5625-40d0-b7ec-e3405ea20279",
722
  "metadata": {},
723
  "outputs": [
 
756
  " <tbody>\n",
757
  " <tr>\n",
758
  " <th>0</th>\n",
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
759
  " <td>SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP...</td>\n",
760
  " <td>OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(...</td>\n",
761
+ " <td>0.2100</td>\n",
762
  " <td>2147484672</td>\n",
763
  " <td>36176898</td>\n",
764
  " <td>850664773</td>\n",
 
767
  " <td>252</td>\n",
768
  " </tr>\n",
769
  " <tr>\n",
770
+ " <th>1</th>\n",
771
  " <td>EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI...</td>\n",
772
  " <td>O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2...</td>\n",
773
+ " <td>0.0500</td>\n",
774
  " <td>0</td>\n",
775
  " <td>1858306115</td>\n",
776
  " <td>4223456596</td>\n",
 
779
  " <td>124</td>\n",
780
  " </tr>\n",
781
  " <tr>\n",
782
+ " <th>2</th>\n",
783
+ " <td>RGSHMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHL...</td>\n",
784
+ " <td>CCNC(=O)c1nc([nH]c(=O)c1O)[C@@H]1CCCN1C(=O)C</td>\n",
785
+ " <td>2.0000</td>\n",
786
+ " <td>0</td>\n",
787
+ " <td>33947650</td>\n",
788
+ " <td>2041877824</td>\n",
789
+ " <td>3782085608</td>\n",
790
+ " <td>4290771792</td>\n",
791
+ " <td>252</td>\n",
792
+ " </tr>\n",
793
+ " <tr>\n",
794
+ " <th>3</th>\n",
795
+ " <td>QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAH...</td>\n",
796
+ " <td>OC[C@H]1O[C@H](C[C@H]([C@@H]1O)F)n1ccc(nc1=O)N...</td>\n",
797
+ " <td>6550.0000</td>\n",
798
+ " <td>0</td>\n",
799
+ " <td>1107566598</td>\n",
800
+ " <td>1755681856</td>\n",
801
+ " <td>3846453088</td>\n",
802
+ " <td>4293647263</td>\n",
803
+ " <td>124</td>\n",
804
+ " </tr>\n",
805
+ " <tr>\n",
806
+ " <th>4</th>\n",
807
+ " <td>YELPEDPRWELPRDRLVLGKPLGEGQVVLAEAIGLDKDKPNRVTKV...</td>\n",
808
+ " <td>C[N@@H+]1CC[N@H+](CC1)Cc1ccc(cc1C(F)(F)F)NC(=O...</td>\n",
809
+ " <td>0.0077</td>\n",
810
+ " <td>4194304</td>\n",
811
+ " <td>4857858</td>\n",
812
+ " <td>515249472</td>\n",
813
+ " <td>3969840044</td>\n",
814
+ " <td>2061460183</td>\n",
815
+ " <td>252</td>\n",
816
+ " </tr>\n",
817
+ " <tr>\n",
818
  " <th>...</th>\n",
819
  " <td>...</td>\n",
820
  " <td>...</td>\n",
 
827
  " <td>...</td>\n",
828
  " </tr>\n",
829
  " <tr>\n",
830
+ " <th>662479</th>\n",
831
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
832
+ " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
833
+ " <td>0.0045</td>\n",
834
+ " <td>65536</td>\n",
835
+ " <td>393216</td>\n",
836
+ " <td>964698368</td>\n",
837
+ " <td>369403648</td>\n",
838
+ " <td>4284858000</td>\n",
839
  " <td>252</td>\n",
840
  " </tr>\n",
841
  " <tr>\n",
842
+ " <th>662480</th>\n",
843
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
844
+ " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
845
+ " <td>0.0045</td>\n",
846
+ " <td>65536</td>\n",
847
+ " <td>393216</td>\n",
848
+ " <td>964698368</td>\n",
849
+ " <td>369403648</td>\n",
850
+ " <td>4284858000</td>\n",
851
  " <td>252</td>\n",
852
  " </tr>\n",
853
  " <tr>\n",
854
+ " <th>662481</th>\n",
 
 
 
 
 
 
 
 
 
 
 
 
855
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
856
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
857
+ " <td>125.0000</td>\n",
858
  " <td>67108864</td>\n",
859
  " <td>1115688962</td>\n",
860
  " <td>1771869508</td>\n",
 
863
  " <td>124</td>\n",
864
  " </tr>\n",
865
  " <tr>\n",
866
+ " <th>662482</th>\n",
867
+ " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
868
+ " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
869
+ " <td>2.0000</td>\n",
870
+ " <td>2097152</td>\n",
871
+ " <td>137216</td>\n",
872
+ " <td>958148868</td>\n",
873
+ " <td>1746307978</td>\n",
874
+ " <td>2067783280</td>\n",
875
+ " <td>204</td>\n",
876
+ " </tr>\n",
877
+ " <tr>\n",
878
+ " <th>662483</th>\n",
879
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
880
  " <td>CC[Se]C(=N)N</td>\n",
881
+ " <td>0.0390</td>\n",
882
  " <td>16</td>\n",
883
  " <td>6144</td>\n",
884
  " <td>537396736</td>\n",
 
888
  " </tr>\n",
889
  " </tbody>\n",
890
  "</table>\n",
891
+ "<p>662484 rows × 9 columns</p>\n",
892
  "</div>"
893
  ],
894
  "text/plain": [
895
+ " seq \\\n",
896
+ "0 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP... \n",
897
+ "1 EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI... \n",
898
+ "2 RGSHMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHL... \n",
899
+ "3 QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAH... \n",
900
+ "4 YELPEDPRWELPRDRLVLGKPLGEGQVVLAEAIGLDKDKPNRVTKV... \n",
901
+ "... ... \n",
902
+ "662479 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
903
+ "662480 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
904
+ "662481 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
905
+ "662482 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
906
+ "662483 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
907
  "\n",
908
+ " smiles affinity_uM \\\n",
909
+ "0 OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(... 0.2100 \n",
910
+ "1 O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2... 0.0500 \n",
911
+ "2 CCNC(=O)c1nc([nH]c(=O)c1O)[C@@H]1CCCN1C(=O)C 2.0000 \n",
912
+ "3 OC[C@H]1O[C@H](C[C@H]([C@@H]1O)F)n1ccc(nc1=O)N... 6550.0000 \n",
913
+ "4 C[N@@H+]1CC[N@H+](CC1)Cc1ccc(cc1C(F)(F)F)NC(=O... 0.0077 \n",
914
+ "... ... ... \n",
915
+ "662479 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
916
+ "662480 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
917
+ "662481 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.0000 \n",
918
+ "662482 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
919
+ "662483 CC[Se]C(=N)N 0.0390 \n",
920
  "\n",
921
+ " 0 1 2 3 4 5 \n",
922
+ "0 2147484672 36176898 850664773 3978479102 1599828989 252 \n",
923
+ "1 0 1858306115 4223456596 4018595822 4282121085 124 \n",
924
+ "2 0 33947650 2041877824 3782085608 4290771792 252 \n",
925
+ "3 0 1107566598 1755681856 3846453088 4293647263 124 \n",
926
+ "4 4194304 4857858 515249472 3969840044 2061460183 252 \n",
927
+ "... ... ... ... ... ... ... \n",
928
+ "662479 65536 393216 964698368 369403648 4284858000 252 \n",
929
+ "662480 65536 393216 964698368 369403648 4284858000 252 \n",
930
+ "662481 67108864 1115688962 1771869508 4018431718 3744193341 124 \n",
931
+ "662482 2097152 137216 958148868 1746307978 2067783280 204 \n",
932
+ "662483 16 6144 537396736 2170880 1510015504 192 \n",
933
  "\n",
934
+ "[662484 rows x 9 columns]"
935
  ]
936
  },
937
+ "execution_count": 24,
938
  "metadata": {},
939
  "output_type": "execute_result"
940
  }
 
945
  },
946
  {
947
  "cell_type": "code",
948
+ "execution_count": 25,
949
  "id": "30f7fff7-3cfe-41c8-97c9-666f3e256222",
950
  "metadata": {},
951
  "outputs": [
 
955
  "Index(['seq', 'smiles', 'affinity_uM', 0, 1, 2, 3, 4, 5], dtype='object')"
956
  ]
957
  },
958
+ "execution_count": 25,
959
  "metadata": {},
960
  "output_type": "execute_result"
961
  }
 
966
  },
967
  {
968
  "cell_type": "code",
969
+ "execution_count": 26,
970
  "id": "16d2b26e-984f-4c71-af19-a3e711ed9ca2",
971
  "metadata": {},
972
  "outputs": [],
 
976
  },
977
  {
978
  "cell_type": "code",
979
+ "execution_count": 27,
980
  "id": "27fa2150-8152-444b-ba5b-24bea39fc098",
981
  "metadata": {},
982
  "outputs": [
 
986
  "Index(['smiles', 'affinity_uM'], dtype='object')"
987
  ]
988
  },
989
+ "execution_count": 27,
990
  "metadata": {},
991
  "output_type": "execute_result"
992
  }
 
997
  },
998
  {
999
  "cell_type": "code",
1000
+ "execution_count": 28,
1001
  "id": "89edacbc-52f3-4a76-90b0-95273f5e53b3",
1002
  "metadata": {},
1003
  "outputs": [],
 
1018
  },
1019
  {
1020
  "cell_type": "code",
1021
+ "execution_count": 30,
1022
  "id": "0cad3882-975d-4693-aad1-63ec26646bd0",
1023
  "metadata": {},
1024
  "outputs": [
 
1037
  },
1038
  {
1039
  "cell_type": "code",
1040
+ "execution_count": 31,
1041
  "id": "c200e29a-3f14-41f4-b620-ccce0eb0d5ce",
1042
  "metadata": {},
1043
  "outputs": [
 
1071
  " <tbody>\n",
1072
  " <tr>\n",
1073
  " <th>0</th>\n",
1074
+ " <td>SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP...</td>\n",
1075
+ " <td>OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(...</td>\n",
1076
+ " <td>0.2100</td>\n",
1077
+ " <td>6.677781</td>\n",
1078
  " </tr>\n",
1079
  " <tr>\n",
1080
  " <th>1</th>\n",
1081
+ " <td>EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI...</td>\n",
1082
+ " <td>O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2...</td>\n",
1083
+ " <td>0.0500</td>\n",
1084
+ " <td>7.301030</td>\n",
1085
  " </tr>\n",
1086
  " <tr>\n",
1087
  " <th>2</th>\n",
1088
+ " <td>RGSHMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHL...</td>\n",
1089
+ " <td>CCNC(=O)c1nc([nH]c(=O)c1O)[C@@H]1CCCN1C(=O)C</td>\n",
1090
+ " <td>2.0000</td>\n",
1091
+ " <td>5.698970</td>\n",
1092
  " </tr>\n",
1093
  " <tr>\n",
1094
  " <th>3</th>\n",
1095
+ " <td>QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAH...</td>\n",
1096
+ " <td>OC[C@H]1O[C@H](C[C@H]([C@@H]1O)F)n1ccc(nc1=O)N...</td>\n",
1097
+ " <td>6550.0000</td>\n",
1098
+ " <td>2.183759</td>\n",
1099
  " </tr>\n",
1100
  " <tr>\n",
1101
  " <th>4</th>\n",
1102
+ " <td>YELPEDPRWELPRDRLVLGKPLGEGQVVLAEAIGLDKDKPNRVTKV...</td>\n",
1103
+ " <td>C[N@@H+]1CC[N@H+](CC1)Cc1ccc(cc1C(F)(F)F)NC(=O...</td>\n",
1104
+ " <td>0.0077</td>\n",
1105
+ " <td>8.113509</td>\n",
1106
  " </tr>\n",
1107
  " <tr>\n",
1108
  " <th>...</th>\n",
 
1112
  " <td>...</td>\n",
1113
  " </tr>\n",
1114
  " <tr>\n",
1115
+ " <th>488472</th>\n",
 
 
 
 
 
 
 
1116
  " <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
1117
+ " <td>CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H...</td>\n",
1118
+ " <td>8.0000</td>\n",
1119
  " <td>5.096910</td>\n",
1120
  " </tr>\n",
1121
  " <tr>\n",
1122
+ " <th>488473</th>\n",
1123
+ " <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
1124
+ " <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
1125
+ " <td>0.0045</td>\n",
1126
+ " <td>8.346787</td>\n",
1127
  " </tr>\n",
1128
  " <tr>\n",
1129
+ " <th>488474</th>\n",
1130
  " <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
1131
  " <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
1132
+ " <td>125.0000</td>\n",
1133
  " <td>3.903090</td>\n",
1134
  " </tr>\n",
1135
  " <tr>\n",
1136
+ " <th>488475</th>\n",
1137
+ " <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
1138
+ " <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
1139
+ " <td>2.0000</td>\n",
1140
+ " <td>5.698970</td>\n",
1141
+ " </tr>\n",
1142
+ " <tr>\n",
1143
+ " <th>488476</th>\n",
1144
  " <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
1145
  " <td>CC[Se]C(=N)N</td>\n",
1146
+ " <td>0.0390</td>\n",
1147
  " <td>7.408935</td>\n",
1148
  " </tr>\n",
1149
  " </tbody>\n",
1150
  "</table>\n",
1151
+ "<p>488477 rows × 4 columns</p>\n",
1152
  "</div>"
1153
  ],
1154
  "text/plain": [
1155
+ " seq \\\n",
1156
+ "0 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVP... \n",
1157
+ "1 EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRI... \n",
1158
+ "2 RGSHMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHL... \n",
1159
+ "3 QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAH... \n",
1160
+ "4 YELPEDPRWELPRDRLVLGKPLGEGQVVLAEAIGLDKDKPNRVTKV... \n",
1161
+ "... ... \n",
1162
+ "488472 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
1163
+ "488473 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
1164
+ "488474 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
1165
+ "488475 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
1166
+ "488476 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
1167
  "\n",
1168
+ " smiles affinity_uM \\\n",
1169
+ "0 OCC[C@@H]1CCCCN1c1cc(NCC2=CC=CN(C2)O)n2c(n1)c(... 0.2100 \n",
1170
+ "1 O[C@@H]1[C@@H](COS(=O)(=O)NC(=O)[C@@H]2CCC[NH2... 0.0500 \n",
1171
+ "2 CCNC(=O)c1nc([nH]c(=O)c1O)[C@@H]1CCCN1C(=O)C 2.0000 \n",
1172
+ "3 OC[C@H]1O[C@H](C[C@H]([C@@H]1O)F)n1ccc(nc1=O)N... 6550.0000 \n",
1173
+ "4 C[N@@H+]1CC[N@H+](CC1)Cc1ccc(cc1C(F)(F)F)NC(=O... 0.0077 \n",
1174
+ "... ... ... \n",
1175
+ "488472 CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H... 8.0000 \n",
1176
+ "488473 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
1177
+ "488474 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.0000 \n",
1178
+ "488475 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
1179
+ "488476 CC[Se]C(=N)N 0.0390 \n",
1180
  "\n",
1181
+ " neg_log10_affinity_M \n",
1182
+ "0 6.677781 \n",
1183
+ "1 7.301030 \n",
1184
+ "2 5.698970 \n",
1185
+ "3 2.183759 \n",
1186
+ "4 8.113509 \n",
1187
+ "... ... \n",
1188
+ "488472 5.096910 \n",
1189
+ "488473 8.346787 \n",
1190
+ "488474 3.903090 \n",
1191
+ "488475 5.698970 \n",
1192
+ "488476 7.408935 \n",
1193
  "\n",
1194
+ "[488477 rows x 4 columns]"
1195
  ]
1196
  },
1197
+ "execution_count": 31,
1198
  "metadata": {},
1199
  "output_type": "execute_result"
1200
  }
 
1205
  },
1206
  {
1207
  "cell_type": "code",
1208
+ "execution_count": 32,
1209
  "id": "7f4027a2-0a5f-47bf-8a34-0c6a73b9b112",
1210
  "metadata": {},
1211
  "outputs": [],
 
1215
  },
1216
  {
1217
  "cell_type": "code",
1218
+ "execution_count": 33,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1219
  "id": "b4b9acd7-7784-492b-9fa3-b7fad9d18a9d",
1220
  "metadata": {},
1221
  "outputs": [
 
1223
  "name": "stdout",
1224
  "output_type": "stream",
1225
  "text": [
1226
+ "INFO: Pandarallel will run on 32 workers.\n",
1227
  "INFO: Pandarallel will use Memory file system to transfer data between the main process and workers.\n"
1228
  ]
1229
  }
 
1235
  },
1236
  {
1237
  "cell_type": "code",
1238
+ "execution_count": 34,
1239
  "id": "eb99774f-9bcc-454d-b5e5-a8470223d6ca",
1240
  "metadata": {},
1241
  "outputs": [],
 
1250
  },
1251
  {
1252
  "cell_type": "code",
1253
+ "execution_count": 35,
1254
  "id": "4d44bd8e-f2e1-44b4-aea7-40b4437baf44",
1255
  "metadata": {},
1256
+ "outputs": [
1257
+ {
1258
+ "name": "stderr",
1259
+ "output_type": "stream",
1260
+ "text": [
1261
+ "<ipython-input-35-c2fe70ccb2b7>:1: SettingWithCopyWarning: \n",
1262
+ "A value is trying to be set on a copy of a slice from a DataFrame.\n",
1263
+ "Try using .loc[row_indexer,col_indexer] = value instead\n",
1264
+ "\n",
1265
+ "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
1266
+ " df['smiles_can'] = df['smiles'].parallel_apply(make_canonical)\n"
1267
+ ]
1268
+ }
1269
+ ],
1270
  "source": [
1271
  "df['smiles_can'] = df['smiles'].parallel_apply(make_canonical)"
1272
  ]
1273
  },
1274
  {
1275
  "cell_type": "code",
1276
+ "execution_count": 36,
1277
  "id": "07ffdeb1-f4fa-4776-9fea-a18439e03d2e",
1278
  "metadata": {},
1279
  "outputs": [],
 
1283
  },
1284
  {
1285
  "cell_type": "code",
1286
+ "execution_count": 37,
1287
  "id": "8f949038-d07d-4d3a-a47e-b825cc9018ca",
1288
  "metadata": {},
1289
  "outputs": [],
 
1293
  },
1294
  {
1295
  "cell_type": "code",
1296
+ "execution_count": 38,
1297
  "id": "0c027988-0b44-4010-ad61-7d70eead1654",
1298
  "metadata": {},
1299
  "outputs": [],
 
1303
  },
1304
  {
1305
  "cell_type": "code",
1306
+ "execution_count": 39,
1307
  "id": "6aeba020-b6ff-4633-902e-4df74463eb2f",
1308
  "metadata": {},
1309
  "outputs": [],
 
1313
  },
1314
  {
1315
  "cell_type": "code",
1316
+ "execution_count": 40,
1317
  "id": "91196eee-5fd0-4aa4-927a-5c1a3f436ac8",
1318
  "metadata": {},
1319
  "outputs": [
1320
  {
1321
  "data": {
1322
  "text/plain": [
1323
+ "(array([6.86202031]), array([2.57502859]))"
1324
  ]
1325
  },
1326
+ "execution_count": 40,
1327
  "metadata": {},
1328
  "output_type": "execute_result"
1329
  }
 
1334
  },
1335
  {
1336
  "cell_type": "code",
1337
+ "execution_count": 43,
1338
+ "id": "56269dcb-e691-4759-949d-7bfdd02f5fd4",
1339
  "metadata": {},
1340
  "outputs": [],
1341
  "source": [
1342
+ "df = df.drop(columns='index')"
1343
  ]
1344
  },
1345
  {
1346
  "cell_type": "code",
1347
+ "execution_count": 45,
1348
  "id": "c6c64066-4032-4247-a8b9-00388176cc7b",
1349
  "metadata": {},
1350
  "outputs": [],
 
1354
  },
1355
  {
1356
  "cell_type": "code",
1357
+ "execution_count": 46,
1358
  "id": "469cf0dd-7b87-4245-973c-2a445e1fcca9",
1359
  "metadata": {},
1360
  "outputs": [
1361
  {
1362
  "data": {
1363
  "text/plain": [
1364
+ "Index(['seq', 'smiles', 'affinity_uM', 'neg_log10_affinity_M', 'smiles_can',\n",
1365
+ " 'affinity'],\n",
1366
  " dtype='object')"
1367
  ]
1368
  },
1369
+ "execution_count": 46,
1370
  "metadata": {},
1371
  "output_type": "execute_result"
1372
  }
 
1377
  },
1378
  {
1379
  "cell_type": "code",
1380
+ "execution_count": 47,
1381
  "id": "d91c0d91-474c-4ab2-9a5e-3b7861f7a832",
1382
  "metadata": {},
1383
  "outputs": [
1384
  {
1385
  "data": {
1386
+ "image/png": "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\n",
1387
  "text/plain": [
1388
  "<Figure size 432x288 with 1 Axes>"
1389
  ]
 
1403
  },
1404
  {
1405
  "cell_type": "code",
1406
+ "execution_count": 48,
1407
+ "id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1408
  "metadata": {},
1409
  "outputs": [
1410
  {
1411
  "data": {
1412
  "text/plain": [
1413
+ "487412"
1414
  ]
1415
  },
1416
+ "execution_count": 48,
1417
  "metadata": {},
1418
  "output_type": "execute_result"
1419
  }
1420
  ],
1421
  "source": [
1422
+ "len(df)"
1423
  ]
1424
  },
1425
  {
1426
  "cell_type": "code",
1427
  "execution_count": null,
1428
+ "id": "462ddcda-33ae-42d5-9ff4-1f3b057618a4",
1429
  "metadata": {},
1430
  "outputs": [],
1431
  "source": []
 
1447
  "name": "python",
1448
  "nbconvert_exporter": "python",
1449
  "pygments_lexer": "ipython3",
1450
+ "version": "3.9.4"
1451
  }
1452
  },
1453
  "nbformat": 4,
data/all.parquet CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:4864292b2aa4e63ffdc28ebdc7baea53a3a396d6e66ccd9927a04885586d160e
3
- size 228485896
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:6dbf2746f88d0b2b7af838e054257d1571c63777d6c012a2c5f980e7e87a3bf8
3
+ size 59045970
moad.ipynb CHANGED
@@ -2,7 +2,7 @@
2
  "cells": [
3
  {
4
  "cell_type": "code",
5
- "execution_count": 3,
6
  "id": "c47a32d8-c857-41de-a70a-cec48046df12",
7
  "metadata": {},
8
  "outputs": [],
@@ -12,19 +12,20 @@
12
  },
13
  {
14
  "cell_type": "code",
15
- "execution_count": 92,
16
  "id": "e0c6bd53-3417-44bd-b1b4-81802b37fbfc",
17
  "metadata": {},
18
  "outputs": [],
19
  "source": [
20
  "df = pd.read_csv('binding_moad/every.csv',header=None,skiprows=2)\n",
21
- "df = df.rename(columns={2:'pdb',3: 'ligand_name', 4: 'ligand_valid', 7: 'affinity_val', 8: 'affinity_unit', 9:'smiles'})\n",
 
22
  "#df = df[df['ligand_valid']!='invalid'].copy()"
23
  ]
24
  },
25
  {
26
  "cell_type": "code",
27
- "execution_count": 93,
28
  "id": "e40b1ddc-9a98-4a3b-b8a6-45e3940a3ea2",
29
  "metadata": {},
30
  "outputs": [],
@@ -34,7 +35,7 @@
34
  },
35
  {
36
  "cell_type": "code",
37
- "execution_count": 94,
38
  "id": "4f00a0d1-78db-4f32-9d12-5e035b70ef98",
39
  "metadata": {},
40
  "outputs": [],
@@ -44,7 +45,17 @@
44
  },
45
  {
46
  "cell_type": "code",
47
- "execution_count": 95,
 
 
 
 
 
 
 
 
 
 
48
  "id": "52c0c66c-1eb0-415b-b019-bc77419ccbd7",
49
  "metadata": {},
50
  "outputs": [],
@@ -68,7 +79,7 @@
68
  },
69
  {
70
  "cell_type": "code",
71
- "execution_count": 96,
72
  "id": "e5b4dd41-1389-408d-bee6-6dbeefc1d5c7",
73
  "metadata": {},
74
  "outputs": [],
@@ -78,7 +89,7 @@
78
  },
79
  {
80
  "cell_type": "code",
81
- "execution_count": 121,
82
  "id": "61b8276c-54fe-4989-af5f-723994e1df7e",
83
  "metadata": {},
84
  "outputs": [],
@@ -94,7 +105,28 @@
94
  },
95
  {
96
  "cell_type": "code",
97
- "execution_count": 124,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
98
  "id": "8bb2dfac-5f11-455c-9dee-3607b47b4232",
99
  "metadata": {},
100
  "outputs": [],
@@ -104,7 +136,59 @@
104
  },
105
  {
106
  "cell_type": "code",
107
- "execution_count": 125,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
108
  "id": "0dc39f62-5b18-4a86-9a44-17d1925da2ad",
109
  "metadata": {},
110
  "outputs": [],
@@ -115,17 +199,17 @@
115
  },
116
  {
117
  "cell_type": "code",
118
- "execution_count": 128,
119
  "id": "6d158a41-64c6-4fa2-92d5-562aa11e8924",
120
  "metadata": {},
121
  "outputs": [],
122
  "source": [
123
- "df_all = df_expand.merge(df_complex,left_on='pdb_ref',right_on='name')"
124
  ]
125
  },
126
  {
127
  "cell_type": "code",
128
- "execution_count": 129,
129
  "id": "901fe6c6-dc8c-4ce4-82c6-1fb0b718287a",
130
  "metadata": {},
131
  "outputs": [],
@@ -135,7 +219,7 @@
135
  },
136
  {
137
  "cell_type": "code",
138
- "execution_count": 130,
139
  "id": "383f9a1c-ffc6-43da-ac5a-5bcb815be28b",
140
  "metadata": {},
141
  "outputs": [
@@ -165,7 +249,7 @@
165
  " <th>pdb</th>\n",
166
  " <th>ligand_name</th>\n",
167
  " <th>ligand_valid</th>\n",
168
- " <th>5</th>\n",
169
  " <th>6</th>\n",
170
  " <th>affinity_val</th>\n",
171
  " <th>affinity_unit</th>\n",
@@ -201,7 +285,7 @@
201
  " <td>NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE...</td>\n",
202
  " </tr>\n",
203
  " <tr>\n",
204
- " <th>2</th>\n",
205
  " <td>NaN</td>\n",
206
  " <td>NaN</td>\n",
207
  " <td>NaN</td>\n",
@@ -221,51 +305,51 @@
221
  " <td>NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE...</td>\n",
222
  " </tr>\n",
223
  " <tr>\n",
224
- " <th>7</th>\n",
225
  " <td>NaN</td>\n",
226
  " <td>NaN</td>\n",
227
  " <td>NaN</td>\n",
228
- " <td>43W:A:902</td>\n",
229
  " <td>valid</td>\n",
230
- " <td>ic50</td>\n",
231
  " <td>=</td>\n",
232
- " <td>580.00</td>\n",
233
- " <td>nM</td>\n",
234
- " <td>C#CCCOP(=O)(O)OP(=O)(O)O</td>\n",
235
  " <td>NaN</td>\n",
236
  " <td>False</td>\n",
237
- " <td>2</td>\n",
238
- " <td>4S3F</td>\n",
239
- " <td>0.580000</td>\n",
240
- " <td>4S3F</td>\n",
241
- " <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
242
  " </tr>\n",
243
  " <tr>\n",
244
- " <th>16</th>\n",
245
  " <td>NaN</td>\n",
246
  " <td>NaN</td>\n",
247
  " <td>NaN</td>\n",
248
- " <td>0CG:A:902</td>\n",
249
  " <td>valid</td>\n",
250
- " <td>ic50</td>\n",
251
  " <td>=</td>\n",
252
- " <td>770.00</td>\n",
253
- " <td>nM</td>\n",
254
- " <td>C#CCOP(=O)(O)OP(=O)(O)O</td>\n",
255
  " <td>NaN</td>\n",
256
  " <td>False</td>\n",
257
- " <td>2</td>\n",
258
- " <td>4S3F</td>\n",
259
- " <td>0.770000</td>\n",
260
- " <td>4S3F</td>\n",
261
- " <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
262
  " </tr>\n",
263
  " <tr>\n",
264
- " <th>17</th>\n",
265
  " <td>NaN</td>\n",
266
  " <td>NaN</td>\n",
267
  " <td>NaN</td>\n",
268
- " <td>ADN:A:901</td>\n",
269
  " <td>valid</td>\n",
270
  " <td>Kd</td>\n",
271
  " <td>=</td>\n",
@@ -301,7 +385,7 @@
301
  " <td>...</td>\n",
302
  " </tr>\n",
303
  " <tr>\n",
304
- " <th>51900</th>\n",
305
  " <td>NaN</td>\n",
306
  " <td>NaN</td>\n",
307
  " <td>NaN</td>\n",
@@ -321,7 +405,7 @@
321
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
322
  " </tr>\n",
323
  " <tr>\n",
324
- " <th>51901</th>\n",
325
  " <td>NaN</td>\n",
326
  " <td>NaN</td>\n",
327
  " <td>NaN</td>\n",
@@ -341,7 +425,7 @@
341
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
342
  " </tr>\n",
343
  " <tr>\n",
344
- " <th>51902</th>\n",
345
  " <td>NaN</td>\n",
346
  " <td>NaN</td>\n",
347
  " <td>NaN</td>\n",
@@ -361,7 +445,7 @@
361
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
362
  " </tr>\n",
363
  " <tr>\n",
364
- " <th>51903</th>\n",
365
  " <td>NaN</td>\n",
366
  " <td>NaN</td>\n",
367
  " <td>NaN</td>\n",
@@ -381,7 +465,7 @@
381
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
382
  " </tr>\n",
383
  " <tr>\n",
384
- " <th>51904</th>\n",
385
  " <td>NaN</td>\n",
386
  " <td>NaN</td>\n",
387
  " <td>NaN</td>\n",
@@ -402,66 +486,79 @@
402
  " </tr>\n",
403
  " </tbody>\n",
404
  "</table>\n",
405
- "<p>25425 rows × 17 columns</p>\n",
406
  "</div>"
407
  ],
408
  "text/plain": [
409
- " 0 1 pdb ligand_name ligand_valid 5 6 affinity_val \\\n",
410
- "0 NaN NaN NaN 2PA:C:613 valid Ki = 0.62 \n",
411
- "2 NaN NaN NaN HAE:C:800 valid Ki = 2.60 \n",
412
- "7 NaN NaN NaN 43W:A:902 valid ic50 = 580.00 \n",
413
- "16 NaN NaN NaN 0CG:A:902 valid ic50 = 770.00 \n",
414
- "17 NaN NaN NaN ADN:A:901 valid Kd = 15.00 \n",
415
- "... ... ... ... ... ... ... .. ... \n",
416
- "51900 NaN NaN NaN MAN NAG:G:1 valid Ka = 7860.00 \n",
417
- "51901 NaN NaN NaN MAN NAG:F:1 valid Ka = 7860.00 \n",
418
- "51902 NaN NaN NaN NGA NAG:F:1 valid Ka = 5910.00 \n",
419
- "51903 NaN NaN NaN NGA NAG:E:1 valid Ka = 5910.00 \n",
420
- "51904 NaN NaN NaN NGA NAG:H:1 valid Ka = 5910.00 \n",
 
 
 
 
 
 
 
 
 
 
 
 
 
421
  "\n",
422
- " affinity_unit smiles 10 \\\n",
423
- "0 nM NP(=O)(N)O NaN \n",
424
- "2 uM CC(=O)NO NaN \n",
425
- "7 nM C#CCCOP(=O)(O)OP(=O)(O)O NaN \n",
426
- "16 nM C#CCOP(=O)(O)OP(=O)(O)O NaN \n",
427
- "17 uM c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... NaN \n",
428
- "... ... ... .. \n",
429
- "51900 M^-1 NaN NaN \n",
430
- "51901 M^-1 NaN NaN \n",
431
- "51902 M^-1 NaN NaN \n",
432
- "51903 M^-1 NaN NaN \n",
433
- "51904 M^-1 NaN NaN \n",
434
  "\n",
435
- " is_sep cum_sum pdb_ref affinity_uM name \\\n",
436
- "0 False 1 6H8J 0.000620 6H8J \n",
437
- "2 False 1 6H8J 2.600000 6H8J \n",
438
- "7 False 2 4S3F 0.580000 4S3F \n",
439
- "16 False 2 4S3F 0.770000 4S3F \n",
440
- "17 False 5 2GL0 15.000000 2GL0 \n",
441
- "... ... ... ... ... ... \n",
442
- "51900 False 10499 2WDB 127.226463 2WDB \n",
443
- "51901 False 10499 2WDB 127.226463 2WDB \n",
444
- "51902 False 10499 2WDB 169.204738 2WDB \n",
445
- "51903 False 10499 2WDB 169.204738 2WDB \n",
446
- "51904 False 10499 2WDB 169.204738 2WDB \n",
447
  "\n",
448
  " seq \n",
449
  "0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
450
- "2 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
451
- "7 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
452
- "16 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
453
- "17 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
454
  "... ... \n",
455
- "51900 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
456
- "51901 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
457
- "51902 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
458
- "51903 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
459
- "51904 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
460
  "\n",
461
- "[25425 rows x 17 columns]"
462
  ]
463
  },
464
- "execution_count": 130,
465
  "metadata": {},
466
  "output_type": "execute_result"
467
  }
@@ -472,7 +569,7 @@
472
  },
473
  {
474
  "cell_type": "code",
475
- "execution_count": 133,
476
  "id": "bebc962b-10f7-478c-8e23-e2d3722e875c",
477
  "metadata": {},
478
  "outputs": [],
@@ -483,7 +580,7 @@
483
  {
484
  "cell_type": "code",
485
  "execution_count": null,
486
- "id": "6ceb8706-273c-4a83-8cda-c7e33fc87e38",
487
  "metadata": {},
488
  "outputs": [],
489
  "source": []
@@ -505,7 +602,7 @@
505
  "name": "python",
506
  "nbconvert_exporter": "python",
507
  "pygments_lexer": "ipython3",
508
- "version": "3.8.10"
509
  }
510
  },
511
  "nbformat": 4,
 
2
  "cells": [
3
  {
4
  "cell_type": "code",
5
+ "execution_count": 14,
6
  "id": "c47a32d8-c857-41de-a70a-cec48046df12",
7
  "metadata": {},
8
  "outputs": [],
 
12
  },
13
  {
14
  "cell_type": "code",
15
+ "execution_count": 24,
16
  "id": "e0c6bd53-3417-44bd-b1b4-81802b37fbfc",
17
  "metadata": {},
18
  "outputs": [],
19
  "source": [
20
  "df = pd.read_csv('binding_moad/every.csv',header=None,skiprows=2)\n",
21
+ "df = df.rename(columns={2:'pdb',3: 'ligand_name', 4: 'ligand_valid', 5: 'affinity_quantity',\n",
22
+ " 7: 'affinity_val', 8: 'affinity_unit', 9:'smiles'})\n",
23
  "#df = df[df['ligand_valid']!='invalid'].copy()"
24
  ]
25
  },
26
  {
27
  "cell_type": "code",
28
+ "execution_count": 25,
29
  "id": "e40b1ddc-9a98-4a3b-b8a6-45e3940a3ea2",
30
  "metadata": {},
31
  "outputs": [],
 
35
  },
36
  {
37
  "cell_type": "code",
38
+ "execution_count": 26,
39
  "id": "4f00a0d1-78db-4f32-9d12-5e035b70ef98",
40
  "metadata": {},
41
  "outputs": [],
 
45
  },
46
  {
47
  "cell_type": "code",
48
+ "execution_count": 27,
49
+ "id": "ebaeb749-656e-4b92-8dbd-2e29eefdcad5",
50
+ "metadata": {},
51
+ "outputs": [],
52
+ "source": [
53
+ "quantities = ['ki','kd','ka','k1/2','kb']"
54
+ ]
55
+ },
56
+ {
57
+ "cell_type": "code",
58
+ "execution_count": 28,
59
  "id": "52c0c66c-1eb0-415b-b019-bc77419ccbd7",
60
  "metadata": {},
61
  "outputs": [],
 
79
  },
80
  {
81
  "cell_type": "code",
82
+ "execution_count": 29,
83
  "id": "e5b4dd41-1389-408d-bee6-6dbeefc1d5c7",
84
  "metadata": {},
85
  "outputs": [],
 
89
  },
90
  {
91
  "cell_type": "code",
92
+ "execution_count": 30,
93
  "id": "61b8276c-54fe-4989-af5f-723994e1df7e",
94
  "metadata": {},
95
  "outputs": [],
 
105
  },
106
  {
107
  "cell_type": "code",
108
+ "execution_count": 31,
109
+ "id": "342c8ef3-6808-471b-baa4-f9bdc7f6e8d6",
110
+ "metadata": {},
111
+ "outputs": [
112
+ {
113
+ "data": {
114
+ "text/plain": [
115
+ "88806"
116
+ ]
117
+ },
118
+ "execution_count": 31,
119
+ "metadata": {},
120
+ "output_type": "execute_result"
121
+ }
122
+ ],
123
+ "source": [
124
+ "len(df_expand)"
125
+ ]
126
+ },
127
+ {
128
+ "cell_type": "code",
129
+ "execution_count": 34,
130
  "id": "8bb2dfac-5f11-455c-9dee-3607b47b4232",
131
  "metadata": {},
132
  "outputs": [],
 
136
  },
137
  {
138
  "cell_type": "code",
139
+ "execution_count": 35,
140
+ "id": "b5c0fa42-b595-4b96-b2d5-57f0031427dc",
141
+ "metadata": {},
142
+ "outputs": [],
143
+ "source": [
144
+ "df_filter = df_expand[df_expand['affinity_quantity'].str.lower().isin(quantities)]"
145
+ ]
146
+ },
147
+ {
148
+ "cell_type": "code",
149
+ "execution_count": 38,
150
+ "id": "27c4865b-5337-48e0-9be7-a913b31cfae1",
151
+ "metadata": {},
152
+ "outputs": [
153
+ {
154
+ "data": {
155
+ "text/plain": [
156
+ "88806"
157
+ ]
158
+ },
159
+ "execution_count": 38,
160
+ "metadata": {},
161
+ "output_type": "execute_result"
162
+ }
163
+ ],
164
+ "source": [
165
+ "len(df_expand)"
166
+ ]
167
+ },
168
+ {
169
+ "cell_type": "code",
170
+ "execution_count": 37,
171
+ "id": "f3daf4ad-0205-48c0-8c38-36aa4eb561e0",
172
+ "metadata": {},
173
+ "outputs": [
174
+ {
175
+ "data": {
176
+ "text/plain": [
177
+ "17724"
178
+ ]
179
+ },
180
+ "execution_count": 37,
181
+ "metadata": {},
182
+ "output_type": "execute_result"
183
+ }
184
+ ],
185
+ "source": [
186
+ "len(df_filter)"
187
+ ]
188
+ },
189
+ {
190
+ "cell_type": "code",
191
+ "execution_count": 47,
192
  "id": "0dc39f62-5b18-4a86-9a44-17d1925da2ad",
193
  "metadata": {},
194
  "outputs": [],
 
199
  },
200
  {
201
  "cell_type": "code",
202
+ "execution_count": 48,
203
  "id": "6d158a41-64c6-4fa2-92d5-562aa11e8924",
204
  "metadata": {},
205
  "outputs": [],
206
  "source": [
207
+ "df_all = df_filter.merge(df_complex,left_on='pdb_ref',right_on='name')"
208
  ]
209
  },
210
  {
211
  "cell_type": "code",
212
+ "execution_count": 49,
213
  "id": "901fe6c6-dc8c-4ce4-82c6-1fb0b718287a",
214
  "metadata": {},
215
  "outputs": [],
 
219
  },
220
  {
221
  "cell_type": "code",
222
+ "execution_count": 50,
223
  "id": "383f9a1c-ffc6-43da-ac5a-5bcb815be28b",
224
  "metadata": {},
225
  "outputs": [
 
249
  " <th>pdb</th>\n",
250
  " <th>ligand_name</th>\n",
251
  " <th>ligand_valid</th>\n",
252
+ " <th>affinity_quantity</th>\n",
253
  " <th>6</th>\n",
254
  " <th>affinity_val</th>\n",
255
  " <th>affinity_unit</th>\n",
 
285
  " <td>NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE...</td>\n",
286
  " </tr>\n",
287
  " <tr>\n",
288
+ " <th>1</th>\n",
289
  " <td>NaN</td>\n",
290
  " <td>NaN</td>\n",
291
  " <td>NaN</td>\n",
 
305
  " <td>NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE...</td>\n",
306
  " </tr>\n",
307
  " <tr>\n",
308
+ " <th>2</th>\n",
309
  " <td>NaN</td>\n",
310
  " <td>NaN</td>\n",
311
  " <td>NaN</td>\n",
312
+ " <td>ADN:A:901</td>\n",
313
  " <td>valid</td>\n",
314
+ " <td>Kd</td>\n",
315
  " <td>=</td>\n",
316
+ " <td>15.00</td>\n",
317
+ " <td>uM</td>\n",
318
+ " <td>c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3...</td>\n",
319
  " <td>NaN</td>\n",
320
  " <td>False</td>\n",
321
+ " <td>5</td>\n",
322
+ " <td>2GL0</td>\n",
323
+ " <td>15.000000</td>\n",
324
+ " <td>2GL0</td>\n",
325
+ " <td>MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV...</td>\n",
326
  " </tr>\n",
327
  " <tr>\n",
328
+ " <th>3</th>\n",
329
  " <td>NaN</td>\n",
330
  " <td>NaN</td>\n",
331
  " <td>NaN</td>\n",
332
+ " <td>ADN:B:902</td>\n",
333
  " <td>valid</td>\n",
334
+ " <td>Kd</td>\n",
335
  " <td>=</td>\n",
336
+ " <td>15.00</td>\n",
337
+ " <td>uM</td>\n",
338
+ " <td>c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3...</td>\n",
339
  " <td>NaN</td>\n",
340
  " <td>False</td>\n",
341
+ " <td>5</td>\n",
342
+ " <td>2GL0</td>\n",
343
+ " <td>15.000000</td>\n",
344
+ " <td>2GL0</td>\n",
345
+ " <td>MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV...</td>\n",
346
  " </tr>\n",
347
  " <tr>\n",
348
+ " <th>4</th>\n",
349
  " <td>NaN</td>\n",
350
  " <td>NaN</td>\n",
351
  " <td>NaN</td>\n",
352
+ " <td>ADN:C:903</td>\n",
353
  " <td>valid</td>\n",
354
  " <td>Kd</td>\n",
355
  " <td>=</td>\n",
 
385
  " <td>...</td>\n",
386
  " </tr>\n",
387
  " <tr>\n",
388
+ " <th>17682</th>\n",
389
  " <td>NaN</td>\n",
390
  " <td>NaN</td>\n",
391
  " <td>NaN</td>\n",
 
405
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
406
  " </tr>\n",
407
  " <tr>\n",
408
+ " <th>17683</th>\n",
409
  " <td>NaN</td>\n",
410
  " <td>NaN</td>\n",
411
  " <td>NaN</td>\n",
 
425
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
426
  " </tr>\n",
427
  " <tr>\n",
428
+ " <th>17684</th>\n",
429
  " <td>NaN</td>\n",
430
  " <td>NaN</td>\n",
431
  " <td>NaN</td>\n",
 
445
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
446
  " </tr>\n",
447
  " <tr>\n",
448
+ " <th>17685</th>\n",
449
  " <td>NaN</td>\n",
450
  " <td>NaN</td>\n",
451
  " <td>NaN</td>\n",
 
465
  " <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
466
  " </tr>\n",
467
  " <tr>\n",
468
+ " <th>17686</th>\n",
469
  " <td>NaN</td>\n",
470
  " <td>NaN</td>\n",
471
  " <td>NaN</td>\n",
 
486
  " </tr>\n",
487
  " </tbody>\n",
488
  "</table>\n",
489
+ "<p>17687 rows × 17 columns</p>\n",
490
  "</div>"
491
  ],
492
  "text/plain": [
493
+ " 0 1 pdb ligand_name ligand_valid affinity_quantity 6 \\\n",
494
+ "0 NaN NaN NaN 2PA:C:613 valid Ki = \n",
495
+ "1 NaN NaN NaN HAE:C:800 valid Ki = \n",
496
+ "2 NaN NaN NaN ADN:A:901 valid Kd = \n",
497
+ "3 NaN NaN NaN ADN:B:902 valid Kd = \n",
498
+ "4 NaN NaN NaN ADN:C:903 valid Kd = \n",
499
+ "... ... ... ... ... ... ... .. \n",
500
+ "17682 NaN NaN NaN MAN NAG:G:1 valid Ka = \n",
501
+ "17683 NaN NaN NaN MAN NAG:F:1 valid Ka = \n",
502
+ "17684 NaN NaN NaN NGA NAG:F:1 valid Ka = \n",
503
+ "17685 NaN NaN NaN NGA NAG:E:1 valid Ka = \n",
504
+ "17686 NaN NaN NaN NGA NAG:H:1 valid Ka = \n",
505
+ "\n",
506
+ " affinity_val affinity_unit \\\n",
507
+ "0 0.62 nM \n",
508
+ "1 2.60 uM \n",
509
+ "2 15.00 uM \n",
510
+ "3 15.00 uM \n",
511
+ "4 15.00 uM \n",
512
+ "... ... ... \n",
513
+ "17682 7860.00 M^-1 \n",
514
+ "17683 7860.00 M^-1 \n",
515
+ "17684 5910.00 M^-1 \n",
516
+ "17685 5910.00 M^-1 \n",
517
+ "17686 5910.00 M^-1 \n",
518
  "\n",
519
+ " smiles 10 is_sep cum_sum \\\n",
520
+ "0 NP(=O)(N)O NaN False 1 \n",
521
+ "1 CC(=O)NO NaN False 1 \n",
522
+ "2 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... NaN False 5 \n",
523
+ "3 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... NaN False 5 \n",
524
+ "4 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... NaN False 5 \n",
525
+ "... ... .. ... ... \n",
526
+ "17682 NaN NaN False 10499 \n",
527
+ "17683 NaN NaN False 10499 \n",
528
+ "17684 NaN NaN False 10499 \n",
529
+ "17685 NaN NaN False 10499 \n",
530
+ "17686 NaN NaN False 10499 \n",
531
  "\n",
532
+ " pdb_ref affinity_uM name \\\n",
533
+ "0 6H8J 0.000620 6H8J \n",
534
+ "1 6H8J 2.600000 6H8J \n",
535
+ "2 2GL0 15.000000 2GL0 \n",
536
+ "3 2GL0 15.000000 2GL0 \n",
537
+ "4 2GL0 15.000000 2GL0 \n",
538
+ "... ... ... ... \n",
539
+ "17682 2WDB 127.226463 2WDB \n",
540
+ "17683 2WDB 127.226463 2WDB \n",
541
+ "17684 2WDB 169.204738 2WDB \n",
542
+ "17685 2WDB 169.204738 2WDB \n",
543
+ "17686 2WDB 169.204738 2WDB \n",
544
  "\n",
545
  " seq \n",
546
  "0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
547
+ "1 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
548
+ "2 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
549
+ "3 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
550
+ "4 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
551
  "... ... \n",
552
+ "17682 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
553
+ "17683 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
554
+ "17684 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
555
+ "17685 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
556
+ "17686 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
557
  "\n",
558
+ "[17687 rows x 17 columns]"
559
  ]
560
  },
561
+ "execution_count": 50,
562
  "metadata": {},
563
  "output_type": "execute_result"
564
  }
 
569
  },
570
  {
571
  "cell_type": "code",
572
+ "execution_count": 51,
573
  "id": "bebc962b-10f7-478c-8e23-e2d3722e875c",
574
  "metadata": {},
575
  "outputs": [],
 
580
  {
581
  "cell_type": "code",
582
  "execution_count": null,
583
+ "id": "49a160d6-4599-488a-ba02-a65a79535f38",
584
  "metadata": {},
585
  "outputs": [],
586
  "source": []
 
602
  "name": "python",
603
  "nbconvert_exporter": "python",
604
  "pygments_lexer": "ipython3",
605
+ "version": "3.9.4"
606
  }
607
  },
608
  "nbformat": 4,
pdbbind.ipynb CHANGED
@@ -10,7 +10,7 @@
10
  },
11
  {
12
  "cell_type": "code",
13
- "execution_count": 16,
14
  "id": "86476f6e-802a-463b-a1b0-2ae228bb92af",
15
  "metadata": {},
16
  "outputs": [],
@@ -20,38 +20,38 @@
20
  },
21
  {
22
  "cell_type": "code",
23
- "execution_count": null,
24
- "id": "0cde27df-2f77-4e62-8c65-7b7a4e76b404",
25
  "metadata": {},
26
  "outputs": [],
27
  "source": [
28
- "complex = pd.read_parquet('')"
 
29
  ]
30
  },
31
  {
32
  "cell_type": "code",
33
- "execution_count": 49,
34
- "id": "9b2be11c-f4bb-4107-af49-abd78052afcf",
35
  "metadata": {},
36
  "outputs": [],
37
  "source": [
38
- "df = pd.read_table('pdbbind/data/plain-text-index/index/INDEX_general_PL_data.2019',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n",
39
- "df = df.rename(columns={'#': 'name','release': 'affinity'})"
40
  ]
41
  },
42
  {
43
  "cell_type": "code",
44
- "execution_count": 50,
45
- "id": "16e0fe44-96aa-4d3a-ae42-3609e895418b",
46
  "metadata": {},
47
  "outputs": [],
48
  "source": [
49
- "from numericalunits import mL, nm"
50
  ]
51
  },
52
  {
53
  "cell_type": "code",
54
- "execution_count": 136,
55
  "id": "3acbca3c-9c0b-43a1-a45e-331bf153bcfa",
56
  "metadata": {},
57
  "outputs": [],
@@ -74,167 +74,81 @@
74
  },
75
  {
76
  "cell_type": "code",
77
- "execution_count": 137,
78
  "id": "58e5748b-2cea-43ff-ab51-85a5021bd50b",
79
  "metadata": {},
80
  "outputs": [],
81
  "source": [
82
- "df['affinity_uM'] = df['affinity'].str.split('[=\\~><]').str[1].apply(to_uM)"
 
83
  ]
84
  },
85
  {
86
  "cell_type": "code",
87
- "execution_count": 138,
88
  "id": "d92f0004-68c1-4487-94b9-56b4fd598de4",
89
  "metadata": {},
90
  "outputs": [
91
  {
92
  "data": {
93
- "text/html": [
94
- "<div>\n",
95
- "<style scoped>\n",
96
- " .dataframe tbody tr th:only-of-type {\n",
97
- " vertical-align: middle;\n",
98
- " }\n",
99
- "\n",
100
- " .dataframe tbody tr th {\n",
101
- " vertical-align: top;\n",
102
- " }\n",
103
- "\n",
104
- " .dataframe thead th {\n",
105
- " text-align: right;\n",
106
- " }\n",
107
- "</style>\n",
108
- "<table border=\"1\" class=\"dataframe\">\n",
109
- " <thead>\n",
110
- " <tr style=\"text-align: right;\">\n",
111
- " <th></th>\n",
112
- " <th>name</th>\n",
113
- " <th>affinity</th>\n",
114
- " <th>affinity_uM</th>\n",
115
- " </tr>\n",
116
- " </thead>\n",
117
- " <tbody>\n",
118
- " <tr>\n",
119
- " <th>1</th>\n",
120
- " <td>3zzf</td>\n",
121
- " <td>Ki=400mM</td>\n",
122
- " <td>4.000000e+05</td>\n",
123
- " </tr>\n",
124
- " <tr>\n",
125
- " <th>2</th>\n",
126
- " <td>3gww</td>\n",
127
- " <td>IC50=355mM</td>\n",
128
- " <td>3.550000e+05</td>\n",
129
- " </tr>\n",
130
- " <tr>\n",
131
- " <th>3</th>\n",
132
- " <td>1w8l</td>\n",
133
- " <td>Ki=320mM</td>\n",
134
- " <td>3.200000e+05</td>\n",
135
- " </tr>\n",
136
- " <tr>\n",
137
- " <th>4</th>\n",
138
- " <td>3fqa</td>\n",
139
- " <td>IC50=320mM</td>\n",
140
- " <td>3.200000e+05</td>\n",
141
- " </tr>\n",
142
- " <tr>\n",
143
- " <th>5</th>\n",
144
- " <td>1zsb</td>\n",
145
- " <td>Kd=250mM</td>\n",
146
- " <td>2.500000e+05</td>\n",
147
- " </tr>\n",
148
- " <tr>\n",
149
- " <th>...</th>\n",
150
- " <td>...</td>\n",
151
- " <td>...</td>\n",
152
- " <td>...</td>\n",
153
- " </tr>\n",
154
- " <tr>\n",
155
- " <th>17675</th>\n",
156
- " <td>7cpa</td>\n",
157
- " <td>Ki=11fM</td>\n",
158
- " <td>1.100000e-08</td>\n",
159
- " </tr>\n",
160
- " <tr>\n",
161
- " <th>17676</th>\n",
162
- " <td>2xuf</td>\n",
163
- " <td>Kd=4.1fM</td>\n",
164
- " <td>4.100000e-09</td>\n",
165
- " </tr>\n",
166
- " <tr>\n",
167
- " <th>17677</th>\n",
168
- " <td>1avd</td>\n",
169
- " <td>Kd=1fM</td>\n",
170
- " <td>1.000000e-09</td>\n",
171
- " </tr>\n",
172
- " <tr>\n",
173
- " <th>17678</th>\n",
174
- " <td>2xui</td>\n",
175
- " <td>Kd=1.0fM</td>\n",
176
- " <td>1.000000e-09</td>\n",
177
- " </tr>\n",
178
- " <tr>\n",
179
- " <th>17679</th>\n",
180
- " <td>2avi</td>\n",
181
- " <td>Kd=0.6fM</td>\n",
182
- " <td>6.000000e-10</td>\n",
183
- " </tr>\n",
184
- " </tbody>\n",
185
- "</table>\n",
186
- "<p>17679 rows × 3 columns</p>\n",
187
- "</div>"
188
- ],
189
  "text/plain": [
190
- " name affinity affinity_uM\n",
191
- "1 3zzf Ki=400mM 4.000000e+05\n",
192
- "2 3gww IC50=355mM 3.550000e+05\n",
193
- "3 1w8l Ki=320mM 3.200000e+05\n",
194
- "4 3fqa IC50=320mM 3.200000e+05\n",
195
- "5 1zsb Kd=250mM 2.500000e+05\n",
196
- "... ... ... ...\n",
197
- "17675 7cpa Ki=11fM 1.100000e-08\n",
198
- "17676 2xuf Kd=4.1fM 4.100000e-09\n",
199
- "17677 1avd Kd=1fM 1.000000e-09\n",
200
- "17678 2xui Kd=1.0fM 1.000000e-09\n",
201
- "17679 2avi Kd=0.6fM 6.000000e-10\n",
202
- "\n",
203
- "[17679 rows x 3 columns]"
204
  ]
205
  },
206
- "execution_count": 138,
207
  "metadata": {},
208
  "output_type": "execute_result"
 
 
 
 
 
 
 
 
 
 
 
 
209
  }
210
  ],
211
  "source": [
212
- "df"
 
 
 
 
 
 
 
 
 
 
213
  ]
214
  },
215
  {
216
  "cell_type": "code",
217
- "execution_count": 139,
218
  "id": "d6dda488-f709-4fe7-b372-080042cf7c66",
219
  "metadata": {},
220
  "outputs": [],
221
  "source": [
222
- "df_complex = pd.read_parquet('data/pdbbind_complex.parquet')"
223
  ]
224
  },
225
  {
226
  "cell_type": "code",
227
- "execution_count": 140,
228
  "id": "df7929e3-c7fd-4e1b-a165-92f8d53b9011",
229
  "metadata": {},
230
  "outputs": [],
231
  "source": [
232
- "df_all = df_complex.merge(df,on='name').drop('affinity',axis=1)"
233
  ]
234
  },
235
  {
236
  "cell_type": "code",
237
- "execution_count": 141,
238
  "id": "4d105c42-0d11-49db-9012-52fafc9cd299",
239
  "metadata": {},
240
  "outputs": [],
@@ -244,17 +158,17 @@
244
  },
245
  {
246
  "cell_type": "code",
247
- "execution_count": 142,
248
  "id": "2955b056-26dd-45fa-8d74-f17661253a9a",
249
  "metadata": {},
250
  "outputs": [
251
  {
252
  "data": {
253
  "text/plain": [
254
- "17652"
255
  ]
256
  },
257
- "execution_count": 142,
258
  "metadata": {},
259
  "output_type": "execute_result"
260
  }
@@ -288,7 +202,7 @@
288
  "name": "python",
289
  "nbconvert_exporter": "python",
290
  "pygments_lexer": "ipython3",
291
- "version": "3.8.10"
292
  }
293
  },
294
  "nbformat": 4,
 
10
  },
11
  {
12
  "cell_type": "code",
13
+ "execution_count": 3,
14
  "id": "86476f6e-802a-463b-a1b0-2ae228bb92af",
15
  "metadata": {},
16
  "outputs": [],
 
20
  },
21
  {
22
  "cell_type": "code",
23
+ "execution_count": 5,
24
+ "id": "9b2be11c-f4bb-4107-af49-abd78052afcf",
25
  "metadata": {},
26
  "outputs": [],
27
  "source": [
28
+ "df = pd.read_table('../binding_datasets/pdbbind/data/plain-text-index/index/INDEX_general_PL_data.2019',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n",
29
+ "df = df.rename(columns={'#': 'name','release': 'affinity'})"
30
  ]
31
  },
32
  {
33
  "cell_type": "code",
34
+ "execution_count": 6,
35
+ "id": "16e0fe44-96aa-4d3a-ae42-3609e895418b",
36
  "metadata": {},
37
  "outputs": [],
38
  "source": [
39
+ "from numericalunits import mL, nm"
 
40
  ]
41
  },
42
  {
43
  "cell_type": "code",
44
+ "execution_count": 13,
45
+ "id": "68983ab8-bf11-4ed6-ba06-f962dbdc077e",
46
  "metadata": {},
47
  "outputs": [],
48
  "source": [
49
+ "quantities = ['ki','kd','ka','k1/2','kb']"
50
  ]
51
  },
52
  {
53
  "cell_type": "code",
54
+ "execution_count": 14,
55
  "id": "3acbca3c-9c0b-43a1-a45e-331bf153bcfa",
56
  "metadata": {},
57
  "outputs": [],
 
74
  },
75
  {
76
  "cell_type": "code",
77
+ "execution_count": 15,
78
  "id": "58e5748b-2cea-43ff-ab51-85a5021bd50b",
79
  "metadata": {},
80
  "outputs": [],
81
  "source": [
82
+ "df['affinity_uM'] = df['affinity'].str.split('[=\\~><]').str[1].apply(to_uM)\n",
83
+ "df['affinity_quantity'] = df['affinity'].str.split('[=\\~><]').str[0]"
84
  ]
85
  },
86
  {
87
  "cell_type": "code",
88
+ "execution_count": 12,
89
  "id": "d92f0004-68c1-4487-94b9-56b4fd598de4",
90
  "metadata": {},
91
  "outputs": [
92
  {
93
  "data": {
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
94
  "text/plain": [
95
+ "<AxesSubplot:>"
 
 
 
 
 
 
 
 
 
 
 
 
 
96
  ]
97
  },
98
+ "execution_count": 12,
99
  "metadata": {},
100
  "output_type": "execute_result"
101
+ },
102
+ {
103
+ "data": {
104
+ "image/png": "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\n",
105
+ "text/plain": [
106
+ "<Figure size 432x288 with 1 Axes>"
107
+ ]
108
+ },
109
+ "metadata": {
110
+ "needs_background": "light"
111
+ },
112
+ "output_type": "display_data"
113
  }
114
  ],
115
  "source": [
116
+ "df['affinity_quantity'].hist()"
117
+ ]
118
+ },
119
+ {
120
+ "cell_type": "code",
121
+ "execution_count": 24,
122
+ "id": "aa358835-55f3-4551-9217-e76a15de4fe8",
123
+ "metadata": {},
124
+ "outputs": [],
125
+ "source": [
126
+ "df_filter = df[df['affinity_quantity'].str.lower().isin(quantities)]"
127
  ]
128
  },
129
  {
130
  "cell_type": "code",
131
+ "execution_count": 25,
132
  "id": "d6dda488-f709-4fe7-b372-080042cf7c66",
133
  "metadata": {},
134
  "outputs": [],
135
  "source": [
136
+ "df_complex = pd.read_parquet('../binding_datasets/data/pdbbind_complex.parquet')"
137
  ]
138
  },
139
  {
140
  "cell_type": "code",
141
+ "execution_count": 26,
142
  "id": "df7929e3-c7fd-4e1b-a165-92f8d53b9011",
143
  "metadata": {},
144
  "outputs": [],
145
  "source": [
146
+ "df_all = df_complex.merge(df_filter,on='name').drop('affinity',axis=1)"
147
  ]
148
  },
149
  {
150
  "cell_type": "code",
151
+ "execution_count": 27,
152
  "id": "4d105c42-0d11-49db-9012-52fafc9cd299",
153
  "metadata": {},
154
  "outputs": [],
 
158
  },
159
  {
160
  "cell_type": "code",
161
+ "execution_count": 28,
162
  "id": "2955b056-26dd-45fa-8d74-f17661253a9a",
163
  "metadata": {},
164
  "outputs": [
165
  {
166
  "data": {
167
  "text/plain": [
168
+ "11099"
169
  ]
170
  },
171
+ "execution_count": 28,
172
  "metadata": {},
173
  "output_type": "execute_result"
174
  }
 
202
  "name": "python",
203
  "nbconvert_exporter": "python",
204
  "pygments_lexer": "ipython3",
205
+ "version": "3.9.4"
206
  }
207
  },
208
  "nbformat": 4,