iMODS: internal coordinates normal mode analysis server
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Título
iMODS: internal coordinates normal mode analysis serverAutoría
Fecha de publicación
2014Editor
Oxford University PressISSN
0305-1048; 1362-4962Cita bibliográfica
LÓPEZ-BLANCO, José Ramón, et al. iMODS: internal coordinates normal mode analysis server. Nucleic acids research, 2014, vol. 42, no W1, p. W271-W276.Tipo de documento
info:eu-repo/semantics/articleVersión de la editorial
http://nar.oxfordjournals.org/content/42/W1/W271.longPalabras clave / Materias
Resumen
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 ... [+]
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. [-]
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Nucleic acids research, 2014, vol. 42, no W1Derechos de acceso
© Oxford University Press
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