<jupyter_start><jupyter_text>Docking Parameters used to perform the Ensemble Docking Procedure1. CDK2 conformations were aligned using the $\alpha$ Carbons of pocket residues.<jupyter_code>import sys
sys.path.append('../..')
from helper_modules.protein_subsequences import *
print("Pocket's residues positions used for the structural alignment:")
get_pocket_residues(sep = ',')<jupyter_output>Pocket's residues positions used for the structural alignment:<jupyter_text>2. All conformations were aligned to the same reference structure: [1fin](https://www.rcsb.org/structure/1FIN).<jupyter_code>import pytraj as pyt
import nglview as nv
ens_traj = pyt.load('../3_Protein_Ensembles_Analysis/PDB_402_cdk2_POCKET_ALL.dcd',
                    top = '../3_Protein_Ensembles_Analysis/1fin_ENS.pdb')
nv.show_pytraj(ens_traj)<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.10035419126328217, 'fraction_numerical': 0.014167650531286895, 'mean_word_length': 6.126050420168068, 'pattern_counts': {'":': 0, '<': 8, '<?xml version=': 0, '>': 8, 'https://': 1, 'lorem ipsum': 0, 'www.': 1, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '2', 'dir': 'jupyter-structured-clean-dedup', 'id': '546248', 'license': 'MIT', 'n_tokens_mistral': 292, 'n_tokens_neox': 270, 'n_words': 64, 'path': 'cdk2/4_Ensemble_docking_results/1_Docking_Parameters_used.ipynb', 'repo_name': 'jRicciL/ml_and_ensemble_docking', 'size': '847'}