Multiple alignment of protein structures in three dimensions

Authors:
Evgeny Krissinel;Kim Henrick
Affiliations:
European Bioinformatics Institute, Hinxton, Cambridge, UK;European Bioinformatics Institute, Hinxton, Cambridge, UK
Venue:
CompLife'05 Proceedings of the First international conference on Computational Life Sciences
Year:
2005

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Abstract

The paper describes the algorithm of multiple alignment of protein structures in 3D used in the EBI-MSD web service SSM (Secondary Structure Matching) located at URL given in the title. Structure alignment is known as a computationally hard procedure, with multiple alignment being considerably harder then a more conventional pairwise alignment. We base our approach on an efficient SSM algorithm for pairwise structure alignment, which allowed for multiple alignment of a considerably larger number of structures (up to 100), on comparison with alternative techniques, in real time.