Cited by 180Protein Structure and DynamicsEnzyme Structure and FunctionComputational Drug Discovery Methods

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

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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  • 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)
Venue
Proceedings of the National Academy of Sciences
Published
1999-07-20
Volume
96
Issue
15
Pages
8477-8482
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
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
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

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