IMODS: internal coordinates normal mode analysis server.

ABSTRACT: 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 r

SUBMITTER: Lopez-Blanco JR 

PROVIDER: S-EPMC4086069 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature