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...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Ivaylo Ilinkin, Jieping Ye, Ravi Janardan
• Keywords: Algorithm, BMCBI 2010, Multiple Structure Alignment, Protein