The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
A novel shape complementarity scoring function for protein‐protein docking
Abstract
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). Proteins 2003;51:397–408. © 2003 Wiley‐Liss, Inc.
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A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706
Principles of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
A protein linkage map of Escherichia coli bacteriophage T7
Bartel, P. L., Roecklein, J. A., SenGupta, D., & Fields, S. (1996) · Nature Genetics · doi:10.1038/ng0196-72 · Cited by 333
A systematic study of low-resolution recognition in protein-protein complexes
Vakser, I. A., Matar, O. G., & Lam, C. F. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.15.8477 · Cited by 180
Cited by
ZDOCK: An initial‐stage protein‐docking algorithm
Chen, R., Li, L., & Weng, Z. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10389 · Cited by 1,393
Self-citationClusPro: an automated docking and discrimination method for the prediction of protein complexes
Comeau, S. R., Gatchell, D. W., Vajda, S., & Camacho, C. J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg371 · Cited by 855
Vreven, T., Moal, I. H., Vangone, A., Pierce, B. G., Kastritis, P. L., Torchala, M., Chaleil, R., Jiménez-García, B., Bates, P. A., Fernandez-Recio, J., et al. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.07.016 · Cited by 424
Self-citationThahsin, N., Khan, K. I., Sarwar, A. N. M. R., Sakib, M. N., & Rahman, M. S. (2025) · Computational and Structural Biotechnology Reports · doi:10.1016/j.csbr.2024.100029 · Cited by 2
Kadam, V., Bhargav, P., & Mukherjee, A. (2026) · Journal of Chemical Sciences · doi:10.1007/s12039-025-02459-7
Metadata
- Authors
- Chen, R., & Weng, Z.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2003-04-08
- Volume
- 51
- Issue
- 3
- Pages
- 397-408
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2118514515
- Cited by
- 298
- References
- 4
- FWCI
- 4.07
- Type
- journal article
- Language
- en
- Open access
- closed
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