title: A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI.
abstract: Protein-protein docking is usually exploited with a two-step strategy, i.e., conformational sampling and decoy scoring. In this work, a new filter enhanced sampling scheme was proposed and added into the RosettaDock algorithm to improve the conformational sampling efficiency. The filter term is based on the statistical result that backbone hydrogen bonds in the native protein structures are wrapped by more than nine hydrophobic groups to shield them from attacks of water molecules (Fernandez and Scheraga, Proc Natl Acad Sci USA 2003;100:113-118). A combinatorial scoring function, ComScore, specially designed for the other-type protein-protein complexes was also adopted to select the near native docked modes. ComScore was composed of the atomic contact energy, van der Waals, and electrostatic interaction energies, and the weight of each item was fit through the multiple linear regression approach. To analyze our docking results, the filter enhanced sampling scheme was applied to targets T12, T20, and T21 after the CAPRI blind test, and improvements were obtained. The ligand least root mean square deviations (L_rmsds) were reduced and the hit numbers were increased. ComScore was used in the scoring test for CAPRI rounds 9-12 with good success in rounds 9 and 11.
authors.affiliation: College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China.
authors.forename: Xin Qi
authors.initials: XQ
authors.lastname: Gong
authors.forename: Shan
authors.initials: S
authors.lastname: Chang
authors.forename: Qing Hua
authors.initials: QH
authors.lastname: Zhang
authors.forename: Chun Hua
authors.initials: CH
authors.lastname: Li
authors.forename: Long Zhu
authors.initials: LZ
authors.lastname: Shen
authors.forename: Xiao Hui
authors.initials: XH
authors.lastname: Ma
authors.forename: Ming Hui
authors.initials: MH
authors.lastname: Wang
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.forename: Hong Qiu
authors.initials: HQ
authors.lastname: He
authors.forename: Wei Zu
authors.initials: WZ
authors.lastname: Chen
authors.forename: Cun Xin
authors.initials: CX
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D023281:Genomics; D008024:Ligands; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software