iMODS: internal coordinates normal mode analysis server
By José Ramón López-Blanco, J. Aliaga, E. Quintana-Ortí, Pablo Chacón. Nucleic Acids Res., 2014
879 citations recorded by the source corpus.
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 animations 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.
Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/beffacadae1177ca3078c67492aac90ec36dc3af
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In Molecular Biology
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In Spectroscopy
Citations in the corpus
- CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures (2018, methodology): “Other computational tools use normal mode analysis (NMA) or various kinds of coarsegrained models (10-14) Their limitations depend on their particular design, especially on the simplifications assumed, and on the modeled system (for example NMA is well suited only for certain systems(15)).”