The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
ZDOCK: An initial‐stage protein‐docking algorithm
Abstract
The development of scoring functions is of great importance to protein docking. Here we present a new scoring function for the initial stage of unbound docking. It combines our recently developed pairwise shape complementarity with desolvation and electrostatics. We compare this scoring function with three other functions on a large benchmark of 49 nonredundant test cases and show its superior performance, especially for the antibody‐antigen category of test cases. For 44 test cases (90% of the benchmark), we can retain at least one near‐native structure within the top 2000 predictions at the 6° rotational sampling density, with an average of 52 near‐native structures per test case. The remaining five difficult test cases can be explained by a combination of poor binding affinity, large backbone conformational changes, and our algorithm's strong tendency for identifying large concave binding pockets. All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at http://zlab.bu.edu/∼rong/dock. Proteins 2003;52:80–87. © 2003 Wiley‐Liss, Inc.
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“conventional approaches for predicting the structure of protein complexes include a docking component8–11, which is limited by force-field accuracy and the completeness of conformational space sampling.”
From AF2Complex predicts direct physical interactions in multimeric proteins with deep learning (2022) · cites this paper as [11]
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Cites
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Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
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Determination of atomic desolvation energies from the structures of crystallized proteins
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Flexible protein–ligand docking by global energy optimization in internal coordinates
Totrov, M. M., & Abagyan, R. A. (1997) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(1997)1+ · Cited by 451
Prediction of protein–protein interactions by docking methods
Smith, G. R., & Sternberg, M. J. E. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00285-3 · Cited by 450
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
Chen, R., & Weng, Z. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10092 · Cited by 375
Self-citationA protein–protein docking benchmark
Chen, R., Mintseris, J., Janin, J., & Weng, Z. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10390 · Cited by 345
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Protein complex prediction with AlphaFold-Multimer
Evans, R., O’Neill, M., Pritzel, A., Antropova, N., Senior, A., Green, T., Žídek, A., Bates, R., Blackwell, S., Yim, J., et al. (2021) · doi:10.1101/2021.10.04.463034 · Cited by 3,808
The ClusPro web server for protein–protein docking
Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S. (2017) · Nature Protocols · doi:10.1038/nprot.2016.169 · Cited by 3,297
Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods
Du, X., Li, Y., Xia, Y.-L., Ai, S.-M., Liang, J., Sang, P., Ji, X., & Liu, S.-Q. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17020144 · Cited by 1,765
Software for molecular docking: a review
Pagadala, N. S., Syed, K., & Tuszynski, J. (2017) · Biophysical Reviews · doi:10.1007/s12551-016-0247-1 · Cited by 1,522
The HADDOCK web server for data-driven biomolecular docking
de Vries, S. J., van Dijk, M., & Bonvin, A. M. J. J. (2010) · Nature Protocols · doi:10.1038/nprot.2010.32 · Cited by 1,387
Metadata
- Authors
- Chen, R., Li, L., & Weng, Z.
- Affiliations
- Boston University (US)
- Corresponding author
- Weng, Zhiping
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2003-05-14
- Volume
- 52
- Issue
- 1
- Pages
- 80-87
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2133712572
- Cited by
- 1,393
- References
- 31
- Citations by year
- 2026: 35 · 2025: 52 · 2024: 67 · 2023: 38 · 2022: 73 · 2021: 75 · 2020: 69 · 2019: 63 · 2018: 57 · 2017: 64 · 2016: 95 · 2015: 66 · 2014: 83 · 2013: 99 · 2012: 69
- FWCI
- 9.19
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- protein docking, scoring functions, ZDOCK, desolvation, electrostatics, antibody-antigen binding, conformational change
- MeSH terms
- Algorithms, Antibodies, Antigens, Binding Sites, Enzyme Inhibitors, Enzymes, Models, Molecular, Proteins, Protein Interaction Mapping, Macromolecular Substances, Static Electricity
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