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dc.contributor.authorDíez Sánchez, Mikel
dc.contributor.authorPetuya Arcocha, Víctor
dc.contributor.authorMartínez Cruz, Luis Alfonso
dc.contributor.authorHernández Frías, Alfonso
dc.date.accessioned2015-12-16T16:30:14Z
dc.date.available2015-12-16T16:30:14Z
dc.date.issued2014-06-12
dc.identifier.citationBMC Bioinformatics 15 : (2014) // Article ID 184es
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/10810/16489
dc.description.abstractBackground: The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein's movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost. Results: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion. Conclusions: The procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.es
dc.description.sponsorshipThe authors wish to acknowledge the financial support received from the Spanish Government through the Ministerio de Economia y Competitividad (Project DPI2011-22955), the Regional Government of the Basque Country through the Departamento de Educacion, Universidades e Investigacion (Project IT445-10) and UPV/EHU under program UFI 11/29 and by Grants from the Department of Education, Universities and Research of the Basque Government (PI2010-17), from the Department of Industry of the Basque Government (ETORTEK Program IE05-147 and IE07-202), from the Bizkaia Country (Exp. 7/13/08/2006/11 and 7/13/08/2005/14), and from the Spanish Ministry of Economy and Innovation (BFU2010-17857 and SICI-CONSOLIDER Program CSD2008-00005) (all to L.A.M.-C.).es
dc.language.isoenges
dc.publisherBiomed Centrales
dc.relationinfo:eu-repo/grantAgreement/MINECO/DPI2011-22955
dc.relationinfo:eu-repo/grantAgreement/MICINN/BFU2010-17857
dc.relationinfo:eu-repo/grantAgreement/MICINN/CSD2008-00005
dc.rightsinfo:eu-repo/semantics/openAccesses
dc.subjectproteines
dc.subjectkinematicses
dc.subjectsimulationes
dc.subjectsecondary structure detectiones
dc.subjectnormal-mode analysises
dc.subjectconformational transitionses
dc.subjectmolecular simulationes
dc.subjectplanning approaches
dc.subjectdynamicses
dc.subjectpolypeptidees
dc.subjectmachineses
dc.subjectgromacses
dc.subjectsolvees
dc.subjectNMAes
dc.titleInsights into mechanism kinematics for protein motion simulationes
dc.typeinfo:eu-repo/semantics/articlees
dc.rights.holder© 2014 Diez et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.es
dc.relation.publisherversionhttp://www.biomedcentral.com/1471-2105/15/184#abses
dc.identifier.doi10.1186/1471-2105-15-184
dc.departamentoesIngeniería mecánicaes_ES
dc.departamentoeuIngeniaritza mekanikoaes_ES
dc.subject.categoriaBIOCHEMISTRY AND MOLECULAR BIOLOGY
dc.subject.categoriaMOLECULAR BIOLOGY
dc.subject.categoriaCOMPUTER SCIENCE APPLICATIONS


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