Multiple Structure Alignment and Consensus Identification for Proteins

  • Jieping Ye
  • Ivaylo Ilinkin
  • Ravi Janardan
  • Adam Isom
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4175)


An algorithm is presented to compute a multiple structure alignment for a set of proteins and to generate a consensus structure which captures common substructures present in the given proteins. 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. A distinguishing feature of the algorithm is that it works directly with the coordinate representation in three dimensions with no loss of spatial information, unlike some other multiple structure alignment algorithms that operate on sets of backbone vectors translated to the origin; hence, the algorithm is able to generate true alignments. Experimental studies on several protein datasets show that the algorithm is quite competitive with a well-known algorithm called CE-MC. A web-based tool has also been developed to facilitate remote access to the algorithm over the Internet.


Structure Alignment Backbone Vector True Alignment Consensus Structure Monte Carlo Optimization 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Jieping Ye
    • 1
  • Ivaylo Ilinkin
    • 2
  • Ravi Janardan
    • 3
  • Adam Isom
    • 3
  1. 1.Arizona State UniversityTempeUSA
  2. 2.Rhodes CollegeMemphisUSA
  3. 3.University of MinnesotaMinneapolisUSA

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