DeepBindRG: a deep learning based method for estimating effective protein-ligand affinity

PeerJ
Haiping ZhangYanjie Wei

Abstract

Proteins interact with small molecules to modulate several important cellular functions. Many acute diseases were cured by small molecule binding in the active site of protein either by inhibition or activation. Currently, there are several docking programs to estimate the binding position and the binding orientation of protein-ligand complex. Many scoring functions were developed to estimate the binding strength and predict the effective protein-ligand binding. While the accuracy of current scoring function is limited by several aspects, the solvent effect, entropy effect, and multibody effect are largely ignored in traditional machine learning methods. In this paper, we proposed a new deep neural network-based model named DeepBindRG to predict the binding affinity of protein-ligand complex, which learns all the effects, binding mode, and specificity implicitly by learning protein-ligand interface contact information from a large protein-ligand dataset. During the initial data processing step, the critical interface information was preserved to make sure the input is suitable for the proposed deep learning model. While validating our model on three independent datasets, DeepBindRG achieves root mean squared error (RMSE) value ...Continue Reading

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Citations

May 14, 2020·Life·Harikrishna Reddy RallabandiYoung Jun Kim
May 23, 2020·International Journal of Molecular Sciences·Neann Mathai, Johannes Kirchmair
Jun 4, 2020·Interdisciplinary Sciences, Computational Life Sciences·Haiping ZhangYanjie Wei
Nov 26, 2020·Chemical Communications : Chem Comm·Jan ZauchaGrzegorz M Popowicz
Dec 11, 2020·Journal of Biomolecular Structure & Dynamics·Karanvir KaushalManisha Naithani
Jan 19, 2021·PeerJ. Computer Science·Christopher A Mirabzadeh, F Marty Ytreberg
Dec 19, 2020·International Journal of Molecular Sciences·Gabriele MacariFabio Polticelli
Mar 24, 2021·Journal of Chemical Information and Modeling·Derek JonesJonathan E Allen
May 1, 2021·International Journal of Molecular Sciences·Talia B KimberAndrea Volkamer
Nov 14, 2020·International Journal of Molecular Sciences·Yongbeom KwonJuyong Lee
Jun 20, 2020·Biomedicine & Pharmacotherapy = Biomédecine & Pharmacothérapie·Xuedong HeCalvin Yu-Chian Chen
Jul 9, 2021·Journal of Medicinal Chemistry·Rocío RecioInmaculada Fernández
Sep 21, 2021·Journal of Biomolecular Structure & Dynamics·Akshaya MurugesanKonda Mani Saravanan
Oct 27, 2021·Briefings in Bioinformatics·Xuxu WeiHongcai Shang
Dec 2, 2021·Briefings in Bioinformatics·Yeji WangYong Huang
Dec 9, 2021·ACS Applied Materials & Interfaces·Cheng YanGuoqiang Li

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Software Mentioned

pafnucy
autodock vina
DeepbindRG
Score
sklearn
Amber
keras
kmeans
ChemScore ChemPLP
Channel Finder

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