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BMCBI
2010

Multiple structure alignment and consensus identification for proteins

9 years 1 days ago
Multiple structure alignment and consensus identification for proteins
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 consensus structures that are visually similar to the input proteins. A comparison with other coordinate-based alignment algorithms (MAMMOTH and MATT) shows that the proposed algorithm is competitive in terms of spee...
Ivaylo Ilinkin, Jieping Ye, Ravi Janardan
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Ivaylo Ilinkin, Jieping Ye, Ravi Janardan
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