Cited by 68Protein Structure and DynamicsEnzyme Structure and FunctionMachine Learning in Bioinformatics

M-TASSER: An Algorithm for Protein Quaternary Structure Prediction

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Chen, Huiling, Skolnick, Jeffrey·2008·Biophysical Journal

Abstract

In a cell, it has been estimated that each protein on average interacts with roughly 10 others, resulting in tens of thousands of proteins known or suspected to have interaction partners; of these, only a tiny fraction have solved protein structures. To partially address this problem, we have developed M-TASSER, a hierarchical method to predict protein quaternary structure from sequence that involves template identification by multimeric threading, followed by multimer model assembly and refinement. The final models are selected by structure clustering. M-TASSER has been tested on a benchmark set comprising 241 dimers having templates with weak sequence similarity and 246 without multimeric templates in the dimer library. Of the total of 207 targets predicted to interact as dimers, 165 (80%) were correctly assigned as interacting with a true positive rate of 68% and a false positive rate of 17%. The initial best template structures have an average root mean-square deviation to native of 5.3, 6.7, and 7.4 A for the monomer, interface, and dimer structures. The final model shows on average a root mean-square deviation improvement of 1.3, 1.3, and 1.5 A over the initial template structure for the monomer, interface, and dimer structures, with refinement evident for 87% of the cases. Thus, we have developed a promising approach to predict full-length quaternary structure for proteins that have weak sequence similarity to proteins of solved quaternary structure.

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Crossref · 10.1529/biophysj.107.114280

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Authors
Chen, H., & Skolnick, J.
Affiliations
Georgia Institute of Technology (US)
Corresponding author
Skolnick, Jeffrey
Venue
Biophysical Journal
Publisher
Elsevier BV
Published
2008-02
Volume
94
Issue
3
Pages
918-928
ISSN
0006-3495 (ISSN-L)
OpenAlex
W2010859992
Cited by
68
References
52
Citations by year
2025: 1 · 2024: 1 · 2023: 5 · 2022: 4 · 2021: 3 · 2020: 4 · 2019: 3 · 2018: 2 · 2017: 1 · 2016: 7 · 2015: 2 · 2014: 3 · 2013: 6 · 2012: 6
FWCI
1.46
Type
journal article
Language
en
Open access
Locations
  • Biophysical Journal (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • SMARTech Repository (Georgia Institute of Technology) (submittedVersion)
Funders
National Institute of General Medical Sciences (GM-48835, R01GM048835)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Keywords
protein dimerization, structure refinement, structural clustering, protein-protein interaction
MeSH terms
Algorithms, Computer Simulation, Models, Chemical, Models, Molecular, Proteins, Software, Protein Structure, Quaternary

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