A systematic study of low-resolution recognition in protein-protein complexes
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A comprehensive nonredundant database of 475 cocrystallized protein-protein complexes was used to study low-resolution recognition, which was reported in earlier docking experiments with a small number of proteins. The docking program GRAMM was used to delete the atom-size structural details and systematically dock the resulting molecular images. The results reveal the existence of the low-resolution recognition in 52% of all complexes in the database and in 76% of the 113 complexes with an interface area >4,000 A(2). Limitations of the docking and analysis tools used in this study suggest that the actual number of complexes with the low-resolution recognition is higher. However, the results already prove the existence of the low-resolution recognition on a broad scale.
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Many modeling techniques needed for a first-pass approximation (e.g., coarse-graining) already exist, requiring proper scaling-up and integration into a self-consistent system.
“Arguably, many modeling techniques needed for a first-pass approximation (e.g. coarse-graining [56–58]) already exist, requiring “just” proper scaling-up and integration into a self-consistent system.”
From Challenges in protein docking (2020) · cites this paper as [56]
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- Authors
- Vakser, I. A., Matar, O. G., & Lam, C. F.
- Affiliations
- Medical University of South Carolina (US)
- ORCID
- Vakser, Ilya A.
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 1999-07-20
- Volume
- 96
- Issue
- 15
- Pages
- 8477-8482
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC17541
- OpenAlex
- W2118459915
- Cited by
- 180
- References
- 39
- Citations by year
- 2024: 1 · 2023: 2 · 2022: 7 · 2021: 3 · 2020: 2 · 2019: 1 · 2018: 4 · 2016: 9 · 2015: 2 · 2014: 4 · 2013: 9 · 2012: 3
- FWCI
- 3.11
- 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)
- 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 complex, protein-protein docking, molecular recognition
- MeSH terms
- Algorithms, Binding Sites, Crystallization, Fourier Analysis, Ligands, Models, Molecular, Protein Binding, Proteins, Receptors, Cell Surface, Protein Structure, Secondary, Protein Structure, Tertiary, Databases as Topic
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.
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