Protein-Protein Docking: From Interaction to Interactome
Open accessAbstract
The protein-protein docking problem is one of the focal points of activity in computational biophysics and structural biology. The three-dimensional structure of a protein-protein complex, generally, is more difficult to determine experimentally than the structure of an individual protein. Adequate computational techniques to model protein interactions are important because of the growing number of known protein structures, particularly in the context of structural genomics. Docking offers tools for fundamental studies of protein interactions and provides a structural basis for drug design. Protein-protein docking is the prediction of the structure of the complex, given the structures of the individual proteins. In the heart of the docking methodology is the notion of steric and physicochemical complementarity at the protein-protein interface. Originally, mostly high-resolution, experimentally determined (primarily by x-ray crystallography) protein structures were considered for docking. However, more recently, the focus has been shifting toward lower-resolution modeled structures. Docking approaches have to deal with the conformational changes between unbound and bound structures, as well as the inaccuracies of the interacting modeled structures, often in a high-throughput mode needed for modeling of large networks of protein interactions. The growing number of docking developers is engaged in the community-wide assessments of predictive methodologies. The development of more powerful and adequate docking approaches is facilitated by rapidly expanding information and data resources, growing computational capabilities, and a deeper understanding of the fundamental principles of protein interactions.
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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 [8]
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Self-citation
- Authors
- Vakser, I. A.
- Affiliations
- University of Kansas (US)
- Corresponding author
- Vakser, Ilya A.
- ORCID
- Vakser, Ilya A.
- Venue
- Biophysical Journal
- Publisher
- Elsevier BV
- Published
- 2014-10
- Volume
- 107
- Issue
- 8
- Pages
- 1785-1793
- ISSN
- 0006-3495 (ISSN-L)
- PMC
- PMC4213718
- OpenAlex
- W2155796229
- Cited by
- 318
- References
- 81
- Citations by year
- 2026: 19 · 2025: 26 · 2024: 33 · 2023: 46 · 2022: 38 · 2021: 31 · 2020: 26 · 2019: 26 · 2018: 25 · 2017: 13 · 2016: 20 · 2015: 14 · 2014: 1
- FWCI
- 1.51
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Biophysical Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM074255)
- 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, protein-protein interaction, protein-protein interaction network, protein-protein complex structure prediction, structural genomics, drug design, conformational change, low-resolution structure, high-throughput docking
- MeSH terms
- Amino Acid Sequence, Animals, Humans, Molecular Sequence Data, Protein Binding, Proteome, Molecular Docking Simulation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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