NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.

ABSTRACT: The NMSim web server implements a three-step approach for multiscale modeling of protein conformational changes. First, the protein structure is coarse-grained using the FIRST software. Second, a rigid cluster normal-mode analysis provides low-frequency normal modes. Third, these modes are used to extend the recently introduced idea of constrained geometric simulations by biasing backbone motions of the protein, whereas side chain motions are biased toward favorable rotamer states (NMSim). The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation.

SUBMITTER: Kruger DM 

PROVIDER: S-EPMC3394247 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature