title: A holistic molecular docking approach for predicting protein-protein complex structure.
abstract: A holistic protein-protein molecular docking approach, HoDock, was established, composed of such steps as binding site prediction, initial complex structure sampling, refined complex structure sampling, structure clustering, scoring and final structure selection. This article explains the detailed steps and applications for CAPRI Target 39. The CAPRI result showed that three predicted binding site residues, A191HIS, B512ARG and B531ARG, were correct, and there were five submitted structures with a high fraction of correct receptor-ligand interface residues, indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.
authors.affiliation: College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
authors.forename: XinQi
authors.initials: X
authors.lastname: Gong
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.forename: Shan
authors.initials: S
authors.lastname: Chang
authors.forename: ChunHua
authors.initials: C
authors.lastname: Li
authors.forename: WeiZu
authors.initials: W
authors.lastname: Chen
authors.forename: CunXin
authors.initials: C
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D046912:Multiprotein Complexes; D011506:Proteins