title: iMod: multipurpose normal mode analysis in internal coordinates.
abstract: BACKGROUND
  Dynamic simulations of systems with biologically relevant sizes and time scales are critical for understanding macromolecular functioning. Coarse-grained representations combined with normal mode analysis (NMA) have been established as an alternative to atomistic simulations. The versatility and efficiency of current approaches normally based on Cartesian coordinates can be greatly enhanced with internal coordinates (IC).
  
  
  RESULTS
  Here, we present a new versatile tool chest to explore conformational flexibility of both protein and nucleic acid structures using NMA in IC. Consideration of dihedral angles as variables reduces the computational cost and non-physical distortions of classical Cartesian NMA methods. Our proposed framework operates at different coarse-grained levels and offers an efficient framework to conduct NMA-based conformational studies, including standard vibrational analysis, Monte-Carlo simulations or pathway exploration. Examples of these approaches are shown to demonstrate its applicability, robustness and efficiency.
  
  
  BACKGROUND
  pablo@chaconlab.org
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute, CSIC, Serrano 119, Madrid 28006, Spain.
authors.forename: José Ramón
authors.initials: JR
authors.lastname: Lopéz-Blanco
authors.forename: José Ignacio
authors.initials: JI
authors.lastname: Garzón
authors.forename: Pablo
authors.initials: P
authors.lastname: Chacón
mesh_terms: D008958:Models, Molecular; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D012984:Software