2024-03-29T07:01:28Zhttps://repositori.uji.es/oai/requestoai:repositori.uji.es:10234/1252072023-07-21T09:33:13Zcom_10234_7036com_10234_9col_10234_8620
00925njm 22002777a 4500
dc
López Blanco, José R.
author
Aliaga Estellés, José Ignacio
author
Quintana-Orti, Enrique S.
author
Chacón, Pablo
author
2014
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.
LÓPEZ-BLANCO, José Ramón, et al. iMODS: internal coordinates normal mode analysis server. Nucleic acids research, 2014, vol. 42, no W1, p. W271-W276.
0305-1048
1362-4962
http://hdl.handle.net/10234/125207
http://dx.doi.org/10.1093/nar/gku339
internal mode analysis
elastic network models
protein flexibility
molecular-dynamics
iMODS: internal coordinates normal mode analysis server