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iMODS: internal coordinates normal mode analysis server
dc.contributor.author | López Blanco, José R. | |
dc.contributor.author | Aliaga Estellés, José Ignacio | |
dc.contributor.author | Quintana-Orti, Enrique S. | |
dc.contributor.author | Chacón, Pablo | |
dc.date.accessioned | 2015-06-25T09:51:42Z | |
dc.date.available | 2015-06-25T09:51:42Z | |
dc.date.issued | 2014 | |
dc.identifier.citation | LÓPEZ-BLANCO, José Ramón, et al. iMODS: internal coordinates normal mode analysis server. Nucleic acids research, 2014, vol. 42, no W1, p. W271-W276. | ca_CA |
dc.identifier.issn | 0305-1048 | |
dc.identifier.issn | 1362-4962 | |
dc.identifier.uri | http://hdl.handle.net/10234/125207 | |
dc.description.abstract | Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animationś and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. | ca_CA |
dc.description.sponsorShip | Human Frontier Science Program—RGP0039/2008, Ministerio de Economía y Competitividad—BFU2013-44306P and Comunidad de Madrid—CAM-S2010/BMD. | ca_CA |
dc.format.extent | 6 p. | ca_CA |
dc.format.mimetype | application/pdf | ca_CA |
dc.language.iso | eng | ca_CA |
dc.publisher | Oxford University Press | ca_CA |
dc.relation.isPartOf | Nucleic acids research, 2014, vol. 42, no W1 | ca_CA |
dc.rights | © Oxford University Press | ca_CA |
dc.rights.uri | http://rightsstatements.org/vocab/InC/1.0/ | * |
dc.subject | internal mode analysis | ca_CA |
dc.subject | elastic network models | ca_CA |
dc.subject | protein flexibility | ca_CA |
dc.subject | molecular-dynamics | ca_CA |
dc.title | iMODS: internal coordinates normal mode analysis server | ca_CA |
dc.type | info:eu-repo/semantics/article | ca_CA |
dc.identifier.doi | http://dx.doi.org/10.1093/nar/gku339 | |
dc.rights.accessRights | info:eu-repo/semantics/openAccess | ca_CA |
dc.relation.publisherVersion | http://nar.oxfordjournals.org/content/42/W1/W271.long | ca_CA |
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