Studying protein–protein interaction through side-chain modeling method OPUS-Mut. Issue 5 (12th August 2022)

• Record Type: Journal Article
• Authors: Xu, Gang; Wang, Yilin; Wang, Qinghua; Ma, Jianpeng
• Is Part Of: Briefings in bioinformatics. Volume 23:Issue 5(2022)
• Publication Date: 2022-08-12
• Subjects: protein side-chain modeling -- protein–protein interaction -- protein–protein docking -- scoring protein–protein docking poses; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbac330
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Protein side chains are vitally important to many biological processes such as protein–protein interaction. In this study, we evaluate the performance of our previous released side-chain modeling method OPUS-Mut, together with some other methods, on three oligomer datasets, CASP14 (11), CAMEO-Homo (65) and CAMEO-Hetero (21). The results show that OPUS-Mut outperforms other methods measured by all residues or by the interfacial residues. We also demonstrate our method on evaluating protein–protein docking pose on a dataset Oligomer-Dock (75) created using the top 10 predictions from ZDOCK 3.0.2. Our scoring function correctly identifies the native pose as the top-1 in 45 out of 75 targets. Different from traditional scoring functions, our method is based on the overall side-chain packing favorableness in accordance with the local packing environment. It emphasizes the significance of side chains and provides a new and effective scoring term for studying protein–protein interaction.