Cited by 1,393Protein Structure and DynamicsComputational Drug Discovery MethodsEnzyme Structure and Function

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ZDOCK: An initial‐stage protein‐docking algorithm

Chen, Rong, Li, Li, Weng, Zhiping·2003·Proteins: Structure, Function, and Bioinformatics

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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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Authors: Chen, R., Li, L., & Weng, Z.
Affiliations: Boston University (US)
Corresponding author: Weng, Zhiping
ORCID: Chen, Rong
Li, Li
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
DOI: 10.1002/prot.10389
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
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
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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ZDOCK: An initial‐stage protein‐docking algorithm

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