• Login
    View Item 
    •   UMB Digital Archive
    • UMB Open Access Articles
    • UMB Open Access Articles 2018
    • View Item
    •   UMB Digital Archive
    • UMB Open Access Articles
    • UMB Open Access Articles 2018
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of UMB Digital ArchiveCommunitiesPublication DateAuthorsTitlesSubjectsThis CollectionPublication DateAuthorsTitlesSubjects

    My Account

    LoginRegister

    Statistics

    Display statistics

    Statistical investigations of protein residue direct couplings

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Author
    Neuwald, A.F.
    Altschul, S.F.
    Date
    2018
    Journal
    PLoS Computational Biology
    Publisher
    Public Library of Science
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://dx.doi.org/10.1371/journal.pcbi.1006237
    Abstract
    Protein Direct Coupling Analysis (DCA), which predicts residue-residue contacts based on covarying positions within a multiple sequence alignment, has been remarkably effective. This suggests that there is more to learn from sequence correlations than is generally assumed, and calls for deeper investigations into DCA and perhaps into other types of correlations. Here we describe an approach that enables such investigations by measuring, as an estimated p-value, the statistical significance of the association between residue-residue covariance and structural interactions, either internal or homodimeric. Its application to thirty protein superfamilies confirms that direct coupling (DC) scores correlate with 3D pairwise contacts with very high significance. This method also permits quantitative assessment of the relative performance of alternative DCA methods, and of the degree to which they detect direct versus indirect couplings. We illustrate its use to assess, for a given protein, the biological relevance of alternative conformational states, to investigate the possible mechanistic implications of differences between these states, and to characterize subtle aspects of direct couplings. Our analysis indicates that direct pairwise correlations may be largely distinct from correlated patterns associated with functional specialization, and that the joint analysis of both types of correlations can yield greater power. Data, programs, and source code are freely available at http://evaldca.igs.umaryland.edu. © 2018, Public Library of Science. All rights reserved. https://creativecommons.org/publicdomain/zero/1.0/.
    Keyword
    direct coupling analysis
    Computational Biology--methods
    Protein Conformation
    Sequence Analysis
    Identifier to cite or link to this item
    https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059525914&doi=10.1371%2fjournal.pcbi.1006237&partnerID=40&md5=4f6cbd6713e94cd387639dd241ad0382; http://hdl.handle.net/10713/8770
    ae974a485f413a2113503eed53cd6c53
    10.1371/journal.pcbi.1006237
    Scopus Count
    Collections
    UMB Open Access Articles 2018

    entitlement

    Related articles

    • Adaptive Smith-Waterman residue match seeding for protein structural alignment.
    • Authors: Topham CM, Rouquier M, Tarrat N, André I
    • Issue date: 2013 Oct
    • Direct coupling analysis for protein contact prediction.
    • Authors: Morcos F, Hwa T, Onuchic JN, Weigt M
    • Issue date: 2014
    • Covariation analysis of local amino acid sequences in recurrent protein local structures.
    • Authors: Wang LY
    • Issue date: 2005 Dec
    • Direct-coupling analysis of residue coevolution captures native contacts across many protein families.
    • Authors: Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M
    • Issue date: 2011 Dec 6
    • From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction.
    • Authors: Cocco S, Monasson R, Weigt M
    • Issue date: 2013
    DSpace software (copyright © 2002 - 2021)  DuraSpace
    Quick Guide | Policies | Contact Us | UMB Health Sciences & Human Services Library
    Open Repository is a service operated by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.