Cited by 213Protein Structure and DynamicsEnzyme Structure and FunctionMachine Learning in Bioinformatics

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Protein Function Prediction Using Local 3D Templates

Laskowski, Roman A., Watson, James D., Thornton, Janet M.·2005·Journal of Molecular Biology

DOI 10.1016/j.jmb.2005.05.067

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Abstract

The prediction of a protein's function from its 3D structure is becoming more and more important as the worldwide structural genomics initiatives gather pace and continue to solve 3D structures, many of which are of proteins of unknown function. Here, we present a methodology for predicting function from structure that shows great promise. It is based on 3D templates that are defined as specific 3D conformations of small numbers of residues. We use four types of template, covering enzyme active sites, ligand-binding residues, DNA-binding residues and reverse templates. The latter are templates generated from the target structure itself and scanned against a representative subset of all known protein structures. Together, the templates provide a fairly thorough coverage of the known structures and ensure that if there is a match to a known structure it is unlikely to be missed. A new scoring scheme provides a highly sensitive means of discriminating between true positive and false positive template matches. In all, the methodology provides a powerful new tool for function prediction to complement those already in use.

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Authors: Laskowski, R. A., Watson, J. D., & Thornton, J. M.
Affiliations: European Bioinformatics Institute (GB)
Corresponding author: Thornton, Janet M.
ORCID: Laskowski, Roman A.
Thornton, Janet M.
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 2005-08
Volume: 351
Issue: 3
Pages: 614-626
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1016/j.jmb.2005.05.067
OpenAlex: W2088534163
Cited by: 213
References: 38
Citations by year: 2026: 6 · 2025: 1 · 2024: 2 · 2023: 5 · 2022: 4 · 2021: 10 · 2020: 6 · 2019: 2 · 2018: 2 · 2017: 8 · 2016: 6 · 2015: 8 · 2014: 11 · 2013: 10 · 2012: 15
FWCI: 8.16
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Funders: European Commission
National Institute of General Medical Sciences (P50GM062414, GM62414)
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 › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Keywords: protein function prediction, 3D templates, enzyme active site, ligand binding residues, DNA-binding residues, template matching, scoring system, structural genomics
MeSH terms: Models, Molecular, Protein Conformation, Proteins, Structure-Activity Relationship

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Protein Function Prediction Using Local 3D Templates

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