The protein-ligand scoring function plays an important role in computer-aided drug discovery, which is heavily used in virtual screening and lead optimization. In this study, we developed a new empirical protein-ligand scoring function, which is a linear combination of empirical energy components, including hydrogen bond, van der Waals, electrostatic, hydrophobic, π-stacking, π-cation, and metal-ligand interaction. Different from previous empirical scoring functions, AA-Score uses several amino acid-specific empirical interaction components. We tested AA-Score on several test sets. The resulting performance shows AA-Score performs well on scoring, docking, and ranking compared with other widely used traditional scoring functions. Our results suggest that AA-Score gains substantial improvements from using detailed protein-ligand interaction components.

• Python 3.6
• Openbabel >= 3.0
• RDKit >= 2019 (http://www.rdkit.org/docs/Install.html)
• numpy 1.18.1
• pandas 0.25.3

This is a example pdb for model prediction, including protein and ligand file:

data/5otc

This tool only support command line. First, you should prepare the protein-ligand complex file, then use the scripts to select binding pocket from protein by referring to the atom position of the ligand.

get_pocket.py or get_pocket_by_schrodinger.py 

The purpose of AA_Score.py is to predict binding affinity by AA-Score:

AA_Score.py
usage: AA_Score.py [-h] [--Rec REC] [--Lig LIG] [--Out OUT]

parse AA Score prediction parameters

optional arguments:
  -h, --help  show this help message and exit
  --Rec REC   the file of binding pocket, only support PDB format
  --Lig LIG   the file of ligands, support mol2, mol, sdf, PDB
  --Out OUT   the output file for recording scores

The purpose of AA_fp.py is to calculate interaction fingerprint by AA-Score:

AA_Fp.py
usage: AA_Fp.py [-h] [--Rec REC] [--Lig LIG] [--Out OUT]

parse AA Score prediction parameters

optional arguments:
  -h, --help  show this help message and exit
  --Rec REC   the file of binding pocket, only support PDB format
  --Lig LIG   the file of ligands, support mol2, mol, sdf, PDB
  --Out OUT   the output file for recording interaction fingerprint

The purpose of the code is to visualize different interactions by AA-Score, including hydrogen bond, pi-pi stacking, pi-cation, salt bridge:

show_interactions.ipynb