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 protein complex structures include a docking component, which is limited by force-field accuracy and completeness of conformational space sampling.
“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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- 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
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Materials Science › Materials Chemistry › 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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