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A systematic study of low-resolution recognition in protein-protein complexes

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Vakser, Ilya A., Matar, Omar G., Lam, Chan F.·1999·Proceedings of the National Academy of Sciences

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Abstract

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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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
DOI: 10.1073/pnas.96.15.8477
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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A systematic study of low-resolution recognition in protein-protein complexes

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