Conformational and functional analysis of molecular dynamics trajectories by self-organising maps.

ABSTRACT:

Background

Molecular dynamics (MD) simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs) were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering.

Results

The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD s

SUBMITTER: Fraccalvieri D 

PROVIDER: S-EPMC3118354 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature