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dc.contributor.authorCarbajo, Daniel
dc.contributor.authorTramontano, Anna
dc.date.accessioned2016-02-21T08:50:07Z
dc.date.available2016-02-21T08:50:07Z
dc.date.issued2012-08-02
dc.identifier.citationCarbajo D, Tramontano A (2012) A resource for benchmarking the usefulness of protein structure models. BMC Bioinformatics 13: 188. Available: http://dx.doi.org/10.1186/1471-2105-13-188.
dc.identifier.issn1471-2105
dc.identifier.pmid22856649
dc.identifier.doi10.1186/1471-2105-13-188
dc.identifier.urihttp://hdl.handle.net/10754/596761
dc.description.abstractBACKGROUND: Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. RESULTS: This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. CONCLUSIONS: The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.
dc.description.sponsorshipThis work was supported by Award number KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST).
dc.publisherSpringer Nature
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttp://creativecommons.org/licenses/by/2.0
dc.subject.meshProtein Conformation
dc.subject.meshModels, Molecular
dc.subject.meshSoftware
dc.subject.meshDatabases, Protein
dc.titleA resource for benchmarking the usefulness of protein structure models.
dc.typeArticle
dc.identifier.journalBMC Bioinformatics
dc.identifier.pmcidPMC3473236
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italy
dc.contributor.institutionInstitut Pasteur - Fondazione Cenci Bolognetti, Rome, Italy
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italy
kaust.grant.numberKUK-I1-012-43
refterms.dateFOA2018-06-13T14:09:00Z
dc.date.published-online2012-08-02
dc.date.published-print2012


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This is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.