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A systematic study of low-resolution recognition in protein-protein complexes
Open accessAbstract
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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“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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PatchDock and SymmDock: servers for rigid and symmetric docking
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Self-citationEfficient Unbound Docking of Rigid Molecules
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Metadata
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › 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
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