Robust probabilistic superposition and comparison of protein structures.

ABSTRACT:

Background

Protein structure comparison is a central issue in structural bioinformatics. The standard dissimilarity measure for protein structures is the root mean square deviation (RMSD) of representative atom positions such as alpha-carbons. To evaluate the RMSD the structures under comparison must be superimposed optimally so as to minimize the RMSD. How to evaluate optimal fits becomes a matter of debate, if the structures contain regions which differ largely--a situation encountered in NMR ensembles and proteins undergoing large-scale conformational transitions.

Results

We present a probabilistic method for robust superposition and comparison of protein structures. Our method aims to identify the largest structurally invariant core. To do so, we model non-rigid displace

SUBMITTER: Mechelke M 

PROVIDER: S-EPMC2912885 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature