A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI
Xin Qi Gong
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Xin Qi Gong and Shan Chang contributed equally to this work.
Search for more papers by this authorShan Chang
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Xin Qi Gong and Shan Chang contributed equally to this work.
Search for more papers by this authorQing Hua Zhang
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorChun Hua Li
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorLong Zhu Shen
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorXiao Hui Ma
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorMing Hui Wang
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorBin Liu
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorHong Qiu He
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorWei Zu Chen
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorCorresponding Author
Cun Xin Wang
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China===Search for more papers by this authorXin Qi Gong
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Xin Qi Gong and Shan Chang contributed equally to this work.
Search for more papers by this authorShan Chang
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Xin Qi Gong and Shan Chang contributed equally to this work.
Search for more papers by this authorQing Hua Zhang
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorChun Hua Li
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorLong Zhu Shen
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorXiao Hui Ma
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorMing Hui Wang
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorBin Liu
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorHong Qiu He
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorWei Zu Chen
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
Search for more papers by this authorCorresponding Author
Cun Xin Wang
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China===Search for more papers by this authorAbstract
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. Proteins 2007. © 2007 Wiley-Liss, Inc.
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