Improving scoring‐docking‐screening powers of protein–ligand scoring functions using random forest

The development of new protein-ligand scoring functions using machine learning algorithms, such as random forest, has been of significant interest. By efficiently utilizing expanded feature sets and a large set of experimental data, random forest based scoring functions (RFbScore) can achieve better correlations to experimental protein-ligand binding data with known crystal structures; however, more extensive tests indicate that such enhancement in scoring power comes with significant under-performance in docking and screening power tests compared to traditional scoring functions. In this work, to improve scoring-docking-screening powers of protein-ligand docking functions simultaneously, we have introduced a Δ vina RF parameterization and feature selection framework based on random forest. Our developed scoring function Δ vina RF 20 , which employs 20 descriptors in addition to the AutoDock Vina score, can achieve superior performance in all power tests of both CASF-2013 and CASF-2007 benchmarks compared to classical scoring functions. The Δ vina RF 20 scoring function and its code are freely available on the web at: https://www.nyu.edu/projects/yzhang/DeltaVina. © 2016 Wiley Periodicals, Inc.