2024-03-29T10:21:01Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/1677392021-11-22T12:49:55Zcom_10261_34com_10261_5col_10261_287
López-Blanco, José R.
Aliaga, Jose I.
Quintana-Ortí, Enrique S.
Chacón, Pablo
2018-07-19T13:22:00Z
2018-07-19T13:22:00Z
2014
Nucleic Acids Research 42: W271- W276 (2014)
http://hdl.handle.net/10261/167739
10.1093/nar/gku339
24771341
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. The server is free and open to all users with no login requirement at http://imods.chaconlab.org. © 2014 The Author(s).
eng
closedAccess
IMODS: Internal coordinates normal mode analysis server
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