Multiple structure alignment and consensus identification for proteins.

ABSTRACT:

Background

An algorithm is presented to compute a multiple structure alignment for a set of proteins and to generate a consensus (pseudo) protein which captures common substructures present in the given proteins. The algorithm represents each protein as a sequence of triples of coordinates of the alpha-carbon atoms along the backbone. It then computes iteratively a sequence of transformation matrices (i.e., translations and rotations) to align the proteins in space and generate the consensus. The algorithm is a heuristic in that it computes an approximation to the optimal alignment that minimizes the sum of the pairwise distances between the consensus and the transformed proteins.

Results

Experimental results show that the algorithm converges quite rapidly and generates cons

SUBMITTER: Ilinkin I 

PROVIDER: S-EPMC2829528 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature