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A novel shape complementarity scoring function for protein‐protein docking
Author(s) -
Chen Rong,
Weng Zhiping
Publication year - 2003
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10334
Subject(s) - docking (animal) , grid , macromolecular docking , pairwise comparison , complementarity (molecular biology) , computer science , benchmark (surveying) , dock , algorithm , protein structure , artificial intelligence , mathematics , biology , geometry , geography , cartography , medicine , biochemistry , genetics , nursing
Shape complementarity is the most basic ingredient of the scoring functions for protein-protein docking. Most grid-based docking algorithms use the total number of grid points at the binding interface to quantify shape complementarity. We have developed a novel Pairwise Shape Complementarity (PSC) function that is conceptually simple and rapid to compute. The favorable component of PSC is the total number of atom pairs between the receptor and the ligand within a distance cutoff. When applied to a benchmark of 49 test cases, PSC consistently ranks near-native structures higher and produces more near-native structures than the traditional grid-based function, and the improvement was seen across all prediction levels and in all categories of the benchmark. Without any post-processing or biological information about the binding site except the complementarity-determining region of antibodies, PSC predicts the complex structure correctly for 6 test cases, and ranks at least one near-native structure in the top 20 predictions for 18 test cases. Our docking program ZDOCK has been parallelized and the average computing time is 4 minutes using sixteen IBM SP3 processors. Both ZDOCK and the benchmark are freely available to academic users (http://zlab.bu.edu/~ rong/dock).