Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation

Proteins
Jianfeng PeiLuhua Lai

Abstract

Solvation energy calculation is one of the main difficulties for the estimation of protein-ligand binding free energy and the correct scoring in docking studies. We have developed a new solvation energy estimation method for protein-ligand binding based on atomic solvation parameter (ASP), which has been shown to improve the power of protein-ligand binding free energy predictions. The ASP set, designed to handle both proteins and organic compounds and derived from experimental n-octanol/water partition coefficient (log P) data, contains 100 atom types (united model that treats hydrogen atoms implicitly) or 119 atom types (all-atom model that treats hydrogen atoms explicitly). By using this unified ASP set, an algorithm was developed for solvation energy calculation and was further integrated into a score function for predicting protein-ligand binding affinity. The score function reproduced the absolute binding free energies of a test set of 50 protein-ligand complexes with a standard error of 8.31 kJ/mol. As a byproduct, a conformation-dependent log P calculation algorithm named ASPLOGP was also implemented. The predictive results of ASPLOGP for a test set of 138 compounds were r = 0.968, s = 0.344 for the all-atom model and r ...Continue Reading

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Citations

Mar 10, 2010·Journal of Molecular Modeling·Jiaying SunYuanqiang Wang
Apr 2, 2010·Journal of Computer-aided Molecular Design·Raphael F RibeiroDonald G Truhlar
Jan 22, 2010·Journal of Chemical Information and Modeling·Sheng-You Huang, Xiaoqin Zou
Jul 27, 2007·Journal of Peptide Science : an Official Publication of the European Peptide Society·Feifei TianZhiliang Li
Apr 26, 2011·Journal of Chemical Information and Modeling·Yaxia YuanLuhua Lai
Sep 3, 2016·Journal of Computer-aided Molecular Design·Diogo Santos-MartinsMaria João Ramos
Oct 26, 2018·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Fernando Jiménez-GrávalosDimas Suárez
Mar 16, 2012·Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering·Kun XieJun Sheng Qi
Feb 19, 2015·Journal of Chemical Theory and Computation·Zheng ZhengKenneth M Merz

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