Protein ligand docking based on empirical method for binding affinity estimation.

P Tao; L Lai

doi:10.1023/a:1011188704521

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PubMed · 11394737

Protein ligand docking based on empirical method for binding affinity estimation.

P Tao·L Lai

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Abstract

An empirical protein-ligand binding affinity estimation method, SCORE, was incorporated into a popular docking program, DOCK4. The combined program, ScoreDock, was used to reconstruct the 200 protein-ligand complex structures and found to give good results for the complexes with high binding affinities. A quality assessment method for docking results from ScoreDock was developed based on the whole test set and tested by additionally selected complexes. The method significantly improves the docking accuracy and was shown to be reliable in docking quality assessment. As a docking tool in structural based drug design, ScoreDock can screen out final hits directly based on the predicted negative logarithms of dissociation equilibrium constants of protein-ligand complexes, and can explicitly deal with structure water molecules, as well as metal atoms.

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Computer Simulation Crystallography, X-Ray Databases as Topic Ligands Models, Molecular Protein Binding Protein Conformation Proteins Software Journal Article Research Support, Non-U.S. Gov't

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P Tao, L Lai. 2001. Protein ligand docking based on empirical method for binding affinity estimation.. https://doi.org/10.1023/a%3A1011188704521

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