A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI.
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.
Gong
Xin Qi
XQ
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China.
Chang
Shan
S
Zhang
Qing Hua
QH
Li
Chun Hua
CH
Shen
Long Zhu
LZ
Ma
Xiao Hui
XH
Wang
Ming Hui
MH
Liu
Bin
B
He
Hong Qiu
HQ
Chen
Wei Zu
WZ
Wang
Cun Xin
CX
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