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ArchDB 2014: structural classification of loops in proteins

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dc.contributor.author Bonet Martínez, Jaume, 1982-
dc.contributor.author Planas Iglesias, Joan, 1980-
dc.contributor.author García-García, Javier, 1982-
dc.contributor.author Marín López, Manuel Alejandro, 1987-
dc.contributor.author Fernández Fuentes, Narcís
dc.contributor.author Oliva Miguel, Baldomero
dc.date.accessioned 2015-03-19T08:02:13Z
dc.date.available 2015-03-19T08:02:13Z
dc.date.issued 2014
dc.identifier.citation Bonet J, Planas-Iglesias J, Garcia-Garcia J, Marín-López MA, Fernandez-Fuentes N, Oliva B. ArchDB 2014: structural classification of loops in proteins. Nucleic Acids Res. 2014;42(Database issue):D315-9. DOI: 10.1093/nar/gkt1189
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10230/23221
dc.description.abstract The function of a protein is determined by its three-dimensional structure, which is formed by regular (i.e. β-strands and α-helices) and non-periodic structural units such as loops. Compared to regular structural elements, non-periodic, non-repetitive conformational units enclose a much higher degree of variability--raising difficulties in the identification of regularities, and yet represent an important part of the structure of a protein. Indeed, loops often play a pivotal role in the function of a protein and different aspects of protein folding and dynamics. Therefore, the structural classification of protein loops is an important subject with clear applications in homology modelling, protein structure prediction, protein design (e.g. enzyme design and catalytic loops) and function prediction. ArchDB, the database presented here (freely available at http://sbi.imim.es/archdb), represents such a resource and has been an important asset for the scientific community throughout the years. In this article, we present a completely reworked and updated version of ArchDB. The new version of ArchDB features a novel, fast and user-friendly web-based interface, and a novel graph-based, computationally efficient, clustering algorithm. The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses.
dc.description.sponsorship This work has been funded by the Spanish Ministry of Science and Innovation (MICINN) [FEDER BIO2008-0205, FEDER BIO2011-22568, EUI2009-04018]; FI-DGR 2012 fellowship from/n‘Generalitat de Catalunya’ (to M.A.M.L.). Funding for open access charge: Spanish Ministry of Science and Innovation
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Nucleic Acids Research. 2014;42(Database issue):D315-9
dc.relation.ispartof Nucleic Acids Research. 2014;42(Database issue):D315-9
dc.rights © 2014 Jaume Bonet et al. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
dc.rights.uri http://creativecommons.org/licenses/by/3.0/
dc.subject.other Proteïnes
dc.title ArchDB 2014: structural classification of loops in proteins
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/nar/gkt1189
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/EUI2009-04018
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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