Commit 422a7ff2 authored by Marta Stepniewska-Dziubinska's avatar Marta Stepniewska-Dziubinska
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Update README.md

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**Pafnucy [paphnusy]** is a 3D convolutional neural network that predicts binding affinity for protein-ligand complexes.
It was trained on the [PDBbind](http://pubs.acs.org/doi/abs/10.1021/acs.accounts.6b00491) database and tested on the [CASF](http://pubs.acs.org/doi/pdf/10.1021/ci500081m) "scoring power" benchmark.
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Save pockets and docked ligands into separate files and use `prepare.py` to create HDF file with atoms' coordinates and features.
By default, script expects mol2 files, but you can use any appropriate file format supported by [Open Babel](http://openbabel.org).
Note that Pafnucy uses protonation and partial charges to calculate features, so make sure that your files contain this information.
If you have a single file with a protein structure, use:
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