iMODS: internal coordinates normal mode analysis server

• Published in: Nucleic acids research Vol. 42; no. Web Server issue; pp. W271 - W276
• Main Authors: López-Blanco, José Ramón, Aliaga, José I, Quintana-Ortí, Enrique S, Chacón, Pablo
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.07.2014
• Subjects: Calcium-Transporting ATPases - chemistry; Chaperonin 10 - chemistry; Chaperonin 60 - chemistry; Internet; Molecular Dynamics Simulation; Protein Conformation; Software
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gku339

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.