Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods.

ABSTRACT:

Background

Obtaining atomic-scale information about large-amplitude conformational transitions in proteins is a challenging problem for both experimental and computational methods. Such information is, however, important for understanding the mechanisms of interaction of many proteins.

Methods

This paper presents a computationally efficient approach, combining methods originating from robotics and computational biophysics, to model protein conformational transitions. The ability of normal mode analysis to predict directions of collective, large-amplitude motions is applied to bias the conformational exploration performed by a motion planning algorithm. To reduce the dimension of the problem, normal modes are computed for a coarse-grained elastic network model built on short

SUBMITTER: Al-Bluwi I 

PROVIDER: S-EPMC3953241 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature