Multiple structure alignment and consensus identification for proteins

Jieping Ye, Ivaylo Ilinkin, Ravi Janardan, Adam Isom

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

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:

Original languageEnglish (US)
Title of host publicationAlgorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings
PublisherSpringer- Verlag
Pages115-125
Number of pages11
ISBN (Print)3540395830, 9783540395836
StatePublished - Jan 1 2006
Event6th International Workshop on Algorithms in Bioinformatics, WABI 2006 - Zurich, Switzerland
Duration: Sep 11 2006Sep 13 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4175 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other6th International Workshop on Algorithms in Bioinformatics, WABI 2006
CountrySwitzerland
CityZurich
Period9/11/069/13/06

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    Ye, J., Ilinkin, I., Janardan, R., & Isom, A. (2006). Multiple structure alignment and consensus identification for proteins. In Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings (pp. 115-125). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4175 LNBI). Springer- Verlag.