A resource for benchmarking the usefulness of protein structure models.

Handle URI:
http://hdl.handle.net/10754/596761
Title:
A resource for benchmarking the usefulness of protein structure models.
Authors:
Carbajo, Daniel; Tramontano, Anna
Abstract:
BACKGROUND: 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.
Citation:
Carbajo 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.
Publisher:
Springer Nature
Journal:
BMC Bioinformatics
KAUST Grant Number:
KUK-I1-012-43
Issue Date:
2-Aug-2012
DOI:
10.1186/1471-2105-13-188
PubMed ID:
22856649
PubMed Central ID:
PMC3473236
Type:
Article
ISSN:
1471-2105
Sponsors:
This work was supported by Award number KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST).
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorCarbajo, Danielen
dc.contributor.authorTramontano, Annaen
dc.date.accessioned2016-02-21T08:50:07Zen
dc.date.available2016-02-21T08:50:07Zen
dc.date.issued2012-08-02en
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.en
dc.identifier.issn1471-2105en
dc.identifier.pmid22856649en
dc.identifier.doi10.1186/1471-2105-13-188en
dc.identifier.urihttp://hdl.handle.net/10754/596761en
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.en
dc.description.sponsorshipThis work was supported by Award number KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST).en
dc.publisherSpringer Natureen
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.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subject.meshProtein Conformationen
dc.subject.meshModels, Molecularen
dc.subject.meshSoftwareen
dc.subject.meshDatabases, Proteinen
dc.titleA resource for benchmarking the usefulness of protein structure models.en
dc.typeArticleen
dc.identifier.journalBMC Bioinformaticsen
dc.identifier.pmcidPMC3473236en
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italyen
dc.contributor.institutionInstitut Pasteur - Fondazione Cenci Bolognetti, Rome, Italyen
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italyen
kaust.grant.numberKUK-I1-012-43en

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