Multiple structure alignment and consensus identification for proteins |
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Authors: | Ivaylo Ilinkin Jieping Ye Ravi Janardan |
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Affiliation: | (1) Department of Computer Science, Gettysburg College, Gettysburg, PA, USA;(2) Department of Computer Science and Engineering, Arizona State University, Tempe, AZ, USA;(3) Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA |
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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. |
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