Cited by 9,652Protein Structure and DynamicsEnzyme Structure and FunctionMachine Learning in Bioinformatics

The Phyre2 web portal for protein modeling, prediction and analysis

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Kelley, Lawrence A, Mezulis, Stefans, Yates, Christopher M, Wass, Mark N, Sternberg, Michael J E·2015·Nature Protocols

Abstract

Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission.

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  • With the exception of the Unknown class, high confidence structural templates were identified for the vast majority of proteins for at least part of the sequence.

    “With the exception of the Unknown class, high confidence structural templates were identified for the vast majority of proteins for at least part of the sequence (Supplementary Fig. 2 and Supplementary Data File 3).”

    From Environmental conditions shape the nature of a minimal bacterial genome (2019) · cites this paper as [11]

    The Introduction’s Phyrealarm section reports that, among 30,000 Phyre2 submissions, more than 50% had over 75% of their sequence modelled with >90% confidence, and another 25% had between a quarter and three quarters confidently modelled. That supports high-confidence matches for at least part of many submitted proteins, but it does not establish the result for the citing paper’s proteins or address its “Unknown” class. No page number is available in our copy. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

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Authors
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. E.
Affiliations
  • Imperial College London (GB)
  • University College London (GB)
  • University of Kent (GB)
Corresponding author
Kelley, Lawrence A
Venue
Nature Protocols
Published
2015-05-07
Volume
10
Issue
6
Pages
845-858
ISSN
  • 1750-2799 (ISSN-L)
  • 1754-2189
OpenAlex
W1803102843
Cited by
9,652
References
36
Citations by year
2026: 250 · 2025: 512 · 2024: 778 · 2023: 902 · 2022: 1173 · 2021: 1401 · 2020: 1278 · 2019: 1062 · 2018: 905 · 2017: 734 · 2016: 529 · 2015: 116 · 2013: 1
FWCI
331.62
Type
journal article
Language
en
Open access
Locations
  • Nature Protocols (publishedVersion)
  • PubMed (publishedVersion)
  • UCL Discovery (University College London) (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Kent Academic Repository (University of Kent) (submittedVersion)
  • Spiral (Imperial College London) (submittedVersion)
Funders
  • Medical Research Council (G1000390-1/1)
  • Biotechnology and Biological Sciences Research Council (BB/F020481/1, BB/J019240/1, BB/M011526/1, BB/G003912/1, BB/G022569/1)
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
Phyre2, protein structure prediction, remote homology detection, protein modeling, ligand binding site prediction, amino acid variants, non-synonymous SNPs, protein function prediction, protein domains, web server, model quality assessment
MeSH terms
Models, Molecular, Protein Conformation, Software, Computational Biology, Internet

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