Multiple structure alignment and consensus identification for proteins
Open Access
- 2 February 2010
- journal article
- Published by Springer Nature in BMC Bioinformatics
- Vol. 11 (1) , 71
Abstract
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.Keywords
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