Protein-protein docking with interface residue restraints

doi:10.1088/1674-1056/abc14e

Abstract The prediction of protein-protein complex structures is crucial for fundamental understanding of celluar processes and drug design. Despite significant progresses in the field, the accuracy of ab initio docking without using any experimental restraints remains relatively low. With the rapid advancement of structural biology, more and more information about binding can be derived from experimental data such as NMR experiments or chemical cross-linking. In addition, information about the residue contacts between proteins may also be derived from their sequences by using evolutionary analysis or deep learning. Here, we propose an efficient approach to incorporate interface residue restraints into protein-protein docking, which is named as HDOCKsite. Extensive evaluations on the protein-protein docking benchmark 4.0 showed that HDOCKsite significantly improved the docking performance and obtained a much higher success rate in binding mode predictions than original ab initio docking.

Keywords: protein-protein interaction scoring function residue restraint molecular docking

Received: 21 July 2020
Revised: 23 September 2020
Accepted manuscript online: 15 October 2020

PACS:	87.15.km	(Protein-protein interactions)
	87.50.cf	(Biophysical mechanisms of interaction)
	05.20.-y	(Classical statistical mechanics)

Fund: Project supported by the National Natural Science Foundation of China (Grant No. 31670724) and the Startup Grant of Huazhong University of Science and Technology.

Corresponding Authors: ^†Corresponding author. E-mail: huangsy@hust.edu.cn

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Hao Li(李豪) and Sheng-You Huang(黄胜友) Protein-protein docking with interface residue restraints 2021 Chin. Phys. B 30 018703

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