柔性多肽片段–蛋白质相互作用的全局对接方法.pdfVIP

Hans Journal of Computational Biology 计算生物学, 2014, 4, 42-50 Published Online June 2014 in Hans. /journal/hjcb /10.12677/hjcb.2014.42005 Global Docking Method for Flexible Peptide Segment-Protein Interactions Ruiying Lai, Bo Wan, Qiang Huang School of Life Sciences, Fudan University, Shanghai Email: rlai11@, huangqiang@ rd th th Received: Jun. 3 , 2014; revised: Jun. 9 , 2014; accepted: Jun. 13 , 2014 Copyright © 2014 by authors and Hans Publishers Inc. This work is licensed under the Creative Commons Attribution International License (CC BY). /licenses/by/4.0/ Abstract Protein-peptide binding plays various important roles in living cells. In many cases, the peptide- binding sites of proteins are not known in prior. Then, computational prediction of the peptide- binding sites is desirable. Popular programs for protein-peptide docking usually depend strongly on the initial positions of peptides, such as Rosetta. To overcome this limitation, here we develop a global docking approach in which the peptide is initially distributed evenly on 26 surface locations of a virtual sphere around the protein, and define a selection parameter for discriminating na- tive-like binding site from non-native sites. We used this approach to predict the native-like bind- ing conformations of peptide-protein complexes, and in most cases the peptide-binding sites were correctly predicted, with Cα-RMSDs below 5.5 Å with respect to the crystal structures of peptides. The results of this study suggested that our approach may be very useful for the identification of peptide-binding sites of proteins. Keywords Protein-Peptide Interaction, Peptide-Binding Site, Molecular Docking 柔性多肽片段–蛋白质相互作用的 全局对接方法