Iterative cluster-NMA: A tool for generating conformational transitions in proteins.

ABSTRACT: Computational models provide insight into the structure-function relationship in proteins. These approaches, especially those based on normal mode analysis, can identify the accessible motion space around a given equilibrium structure. The large magnitude, collective motions identified by these methods are often well aligned with the general direction of the expected conformational transitions. However, these motions cannot realistically be extrapolated beyond the local neighborhood of the starting conformation. In this article, the iterative cluster-NMA (icNMA) method is presented for traversing the energy landscape from a starting conformation to a desired goal conformation. This is accomplished by allowing the evolving geometry of the intermediate structures to define the local accessib

SUBMITTER: Schuyler AD 

PROVIDER: S-EPMC2930202 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature