ClusPro-DC: dimer classification by the Cluspro server for protein–protein docking
Open accessAbstract
ClusPro-DC (https://cluspro.bu.edu/) implements a straightforward approach to the discrimination between crystallographic and biological dimers by docking the two subunits to exhaustively sample the interaction energy landscape. If a substantial number of low energy docked poses cluster in a narrow vicinity of the native structure of the dimer, then one can assume that there is a well-defined free energy well around the native state, which makes the interaction stable. In contrast, if the interaction sites in the docked poses do not form a large enough cluster around the native structure, then it is unlikely that the subunits form a stable biological dimer. The number of near-native structures is used to estimate the probability of a dimer being biological. Currently, the server examines only the stability of a given interface rather than generating all putative quaternary structures as accomplished by PISA or EPPIC, but it complements the information provided by these methods.
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Studies have shown that exploration of the intermolecular energy landscapes based on the docking output is helpful in distinguishing interacting and non-interacting proteins.
“Since these landscapes should be different for strongly and weakly interacting proteins, studies have shown that exploration of the intermolecular energy landscapes based on the docking output is helpful in distinguishing interacting and non-interacting proteins [45,46].”
From Challenges in protein docking (2020) · cites this paper as [45]
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- Authors
- Yueh, C., Hall, D. R., Xia, B., Padhorny, D., Kozakov, D., & Vajda, S.
- Affiliations
- Boston University (US)
- Acpharis (US)
- Stony Brook University (US)
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2017-02
- Volume
- 429
- Issue
- 3
- Pages
- 372-381
- ISSN
- 0022-2836 (ISSN-L)
- PMC
- PMC5538892
- OpenAlex
- W2533605840
- Cited by
- 53
- References
- 25
- Citations by year
- 2026: 5 · 2025: 9 · 2024: 11 · 2023: 4 · 2022: 6 · 2021: 5 · 2020: 4 · 2019: 3 · 2018: 2 · 2017: 2 · 2016: 2
- FWCI
- 1.56
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Journal of Molecular Biology (acceptedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health/ National Institute of General Medical Sciences (R35-GM118078, R01-GM061867)
- National Science FoundationNational Science Foundation (NSF) (DBI 1458509)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein-protein docking, interfacial stability, quaternary structure
- MeSH terms
- Escherichia coli, Protein Conformation, Proteins, X-Rays, Protein Interaction Mapping, Databases, Protein, Molecular Docking Simulation
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