Improving classical scoring functions using random forest: The non-additivity of free energy terms’ contributions in binding
Date
2018
Authors
Journal Title
Journal ISSN
Volume Title
Type
Article
Publisher
Blackwell Publishing Ltd
Series Info
Chemical Biology and Drug Design
92
92
Scientific Journal Rankings
Abstract
Despite recent efforts to improve the scoring performance of scoring functions, accurately predicting the binding affinity is still a challenging task. Therefore, different approaches were tried to improve the prediction performance of four scoring functions (x-score, vina, autodock, and rf-score) by substituting the linear regression model of classical scoring function by random forest to examine the performance improvement if an additive functional form is not imposed, and by combining different scoring functions into hybrid ones. The datasets were derived from the PDBbind-CN database version 2016. When evaluating the original scoring functions on the generic dataset, rf-score has outperformed classical scoring functions, which shows the superiority of descriptor-based scoring functions. Substituting linear regression as a linear model by random forest as a nonlinear model had largely improved the scoring performance of autodock and vina while x-score had only a slight performance increase. All hybrid scoring functions had only a slight improvement�if any�on both of the combined scoring functions, which is not worth the slower calculation time. � 2018 John Wiley & Sons A/S
Description
Scopus
Keywords
autodock, autodock vina, docking, drug design, rf-score, scoring, scoring function, virtual screening, x-score, Article, binding affinity, calculation, data base, energy, hybrid, linear regression analysis, prediction, priority journal, random forest, scoring system, statistical model, chemistry, drug design, entropy, metabolism, molecular docking, ligand, protein, protein binding, Drug Design, Entropy, Ligands, Molecular Docking Simulation, Protein Binding, Proteins