README.md

## How to use the data sets

### Use the already preprocessed data

The file `data/all.parquet` contains the preprocessed data. Load the dataset using

```
from datasets import load_dataset
dataset = load_dataset("jglaser/binding_affinity")
```

### Pre-process yourself

To manually perform the preprocessing, fownload the data sets from

1. BindingDB

In `bindingdb`, download the database as tab separated values
[https://bindingdb.org] > Download > BindingDB_All_2021m4.tsv.zip
and extract the zip archive into `bindingdb/data`

Run the steps in `bindingdb.ipynb`

2. PDBBind-cn

Register for an account at [https://www.pdbbind.org.cn/], confirm the validation
email, then login and download 

- the Index files (1)
- the general protein-ligand complexes (2)
- the refined protein-ligand complexes (3)

Extract those files in `pdbbind/data`

Run the script `pdbbind.py` in a compute job on an MPI-enabled cluster
(e.g., `mpirun -n 64 pdbbind.py`).

Perform the steps in the notebook `pdbbind.ipynb`

3. BindingMOAD

Go to [https://bindingmoad.org] and download the files `every.csv`
(All of Binding MOAD, Binding Data) and the non-redundant biounits
(`nr_bind.zip`). Place and extract those files into `binding_moad`.

Run the script `moad.py` in a compute job on an MPI-enabled cluster
(e.g., `mpirun -n 64 moad.py).

Perform the steps in the notebook `moad.ipynb`

4. BioLIP

Download from [https://zhanglab.ccmb.med.umich.edu/BioLiP/] the files
- receptor_nr1.tar.bz2 (Receptor1, Non-redudant set)
- ligand_nr.tar.bz2 (Ligands)
- BioLiP_nr.tar.bz2 (Annotations)
and extract them in `biolip/data`.

Run the script `biolip.py` in a compute job on an MPI-enabled cluster
(e.g., `mpirun -n 64 biolip.py).

Perform sthe steps in the notebook `biolip.ipynb`

5. Final concatenation and filtering

Run the steps in the notebook `combine_dbs.ipynb`