Templates are available to model nearly all complexes of structurally characterized proteins
Open accessAbstract
Traditional approaches to protein-protein docking sample the binding modes with no regard to similar experimentally determined structures (templates) of protein-protein complexes. Emerging template-based docking approaches utilize such similar complexes to determine the docking predictions. The docking problem assumes the knowledge of the participating proteins' structures. Thus, it provides the possibility of aligning the structures of the proteins and the template complexes. The progress in the development of template-based docking and the vast experience in template-based modeling of individual proteins show that, generally, such approaches are more reliable than the free modeling. The key aspect of this modeling paradigm is the availability of the templates. The current common perception is that due to the difficulties in experimental structure determination of protein-protein complexes, the pool of docking templates is insignificant, and thus a broad application of template-based docking is possible only at some future time. The results of our large scale, systematic study show that, surprisingly, in spite of the limited number of protein-protein complexes in the Protein Data Bank, docking templates can be found for complexes representing almost all the known protein-protein interactions, provided the components themselves have a known structure or can be homology-built. About one-third of the templates are of good quality when they are compared to experimental structures in test sets extracted from the Protein Data Bank and would be useful starting points in modeling the complexes. This finding dramatically expands our ability to model protein interactions, and has far-reaching implications for the protein docking field in general.
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The rise of comparative modeling of protein-protein complexes (template-based docking), based on the rapid expansion of PDB, makes the availability of templates for docking procedures routine.
“The rise of the comparative modeling of protein-protein complexes (template-based docking), based on the rapid expansion of PDB, makes the availability of templates for docking procedures routine [12,13].”
From Challenges in protein docking (2020) · cites this paper as [12]
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- Authors
- Kundrotas, P. J., Zhu, Z., Janin, J., & Vakser, I. A.
- Affiliations
- University of Kansas (US)
- University of California San Diego (US)
- Université Paris-Sud (FR)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2012-05-29
- Volume
- 109
- Issue
- 24
- Pages
- 9438-9441
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3386081
- OpenAlex
- W2163614321
- Cited by
- 179
- References
- 34
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 3 · 2023: 7 · 2022: 16 · 2021: 11 · 2020: 18 · 2019: 14 · 2018: 12 · 2017: 16 · 2016: 22 · 2015: 9 · 2014: 18 · 2013: 20 · 2012: 3
- FWCI
- 6.42
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (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
- template-based docking, protein-protein docking, protein-protein complex, Protein Data Bank, protein-protein interaction, homology modeling, structural alignment
- MeSH terms
- Models, Molecular, Proteins, Databases, Protein
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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