The Phyre2 web portal for protein modelling, prediction and analysis

Article, Other literature type, Unknown English OPEN
Kelley, Lawrence A ; Mezulis, Stefans ; Yates, Christopher M ; Wass, Mark N ; Sternberg, Michael JE (2015)
  • Publisher: Nature Publishing Group
  • Related identifiers: doi: 10.1038/nprot.2015.053
  • Subject: Q1 | Article
    acm: ComputingMethodologies_PATTERNRECOGNITION

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. a typical structure prediction will be returned between 30 min and 2 h after submission.
  • References (35)
    35 references, page 1 of 4

    1. Srayanta Mukherjee, Andras Szilagyi, Ambrish Roy, Yang Zhang. Genome-wide protein structure prediction. Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies, Chapter 11, Edited by Andrzej Kolinski, (Springer-London, 2010), P. 255-280.

    2. Koonin, E.V. et al. The structure of the protein universe and genome evolution. Nature 420, 218-223 (2002).

    3. Kelley, L.A. and Sternberg M.J.E. Protein structure prediction on the web: a case study using the Phyre server. Nat. Protoc. 4, 363 - 371 (2009).

    4. Mao C, et al. Functional assignment of Mycobacterium tuberculosis proteome by genome-scale fold-recognition. Tuberculosis 1, 93 (2013).

    5. Lewis TE, et al. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucl. Acids Res. 41 (D1), D499-D507 (2013).

    6. Fucile G, et al. ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web. PLoS ONE 6(1): e15237 (2010).

    7. Moult, J. et al. Critical assessment of methods of protein structure prediction (CASP)—round X. Proteins 82.S2, 1-6 (2014).

    8. Roy A. et al. I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 5, 725-738 (2010)

    9. Arnold K. et al. The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics 22,195-201. (2006).

    10. Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951-960 (2005).

  • Related Research Results (1)
  • Similar Research Results (2)
  • Metrics
    No metrics available