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Chin. Phys. B, 2021, Vol. 30(1): 018703    DOI: 10.1088/1674-1056/abc14e
Special Issue: SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids
SPECIAL TOPIC—Modeling and simulations for the structures and functions of proteins and nucleic acids Prev   Next  

Protein-protein docking with interface residue restraints

Hao Li(李豪) and Sheng-You Huang(黄胜友)†
School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
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   

Cite this article: 

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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