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--- |
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tags: |
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- molecules |
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- chemistry |
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- SMILES |
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--- |
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## How to use the data sets |
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This dataset contains more than 16,000 unique pairs of protein sequences and ligand SMILES, and the coordinates |
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of their complexes. |
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SMILES are assumed to be tokenized by the regex from P. Schwaller |
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Every (x,y,z) ligand coordinate maps onto a SMILES token, and is *nan* if the token does not represent an atom |
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Every receptor coordinate maps onto the Calpha coordinate of that residue. |
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The dataset can be used to fine-tune a language model, all data comes from PDBind-cn. |
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### Use the already preprocessed data |
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Load a test/train split using |
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``` |
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from datasets import load_dataset |
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train = load_dataset("jglaser/pdbbind_complexes",split='train[:90%]') |
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validation = load_dataset("jglaser/pdbbind_complexes",split='train[90%:]') |
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``` |
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### Pre-process yourself |
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To manually perform the preprocessing, download the data sets from P.DBBind-cn |
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Register for an account at <https://www.pdbbind.org.cn/>, confirm the validation |
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email, then login and download |
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- the Index files (1) |
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- the general protein-ligand complexes (2) |
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- the refined protein-ligand complexes (3) |
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Extract those files in `pdbbind/data` |
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Run the script `pdbbind.py` in a compute job on an MPI-enabled cluster |
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(e.g., `mpirun -n 64 pdbbind.py`). |
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