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                          科學研究

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                          Studying protein–protein interaction through side-chain modeling method OPUS-Mut

                          發表會議及期刊:Briefings in Bioinformatics

                          GangXu,YilinWang,QinghuaWang and JianpengMa

                          Correspondingauthor:Jianpeng Ma,Multiscale Research Institute of Complex Systems,Fudan University,Shanghai,200433,China.

                          E-mail:jpma@fudan.edu.cn



                          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.


                          comm@pjlab.org.cn

                          上海市徐匯區云錦路701號西岸國際人工智能中心37-38層

                          滬ICP備2021009351號-1

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