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Bioinformatics Advance Access published online on October 12, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm499
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Conformational analysis of alternative protein structures

Francisco S. Domingues a,*, Jörg Rahnenführer b and Thomas Lengauer a

aMax-Planck-Institut Informatik, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany,
bFachbereich Statistik, Universität Dortmund,Vogelpothsweg 87,44221 Dortmund, Germany

*To whom correspondence should be addressed. Dr. Francisco S. Domingues, E-mail: doming{at}mpi-sb.mpg.de


  Abstract

Motivation: Alternative structural models determined experimentally are available for an increasing number of proteins. Structural and functional studies of these proteins need to take these models into consideration as they can present considerable structural differences. The characterisation of the structural differences and similarities between these models is a fundamental task in structural biology requiring appropriate methods.

Results: We propose a method for characterising sets of alternative structural models. Three types of analysis are performed: grouping according to structural similarity, visualisation and detection of structural variation, and comparison of subsets for identifying and locating distinct conformational states. The alpha carbon atoms are used in order to analyse the backbone conformations. Alternatively, sidechain atoms are used for detailed conformational analysis of specific sites. The method takes into account estimates of atom coordinate uncertainty. The invariant regions are used to generate optimal superpositions of these models. We present the results obtained for three proteins showing different degrees of conformational variability: relative motion of two structurally conserved subdomains, a disordered subdomain and flexibility in the functional site associated with ligand binding. The method has been applied in the analysis of the alternative models available in SCOP. Considerable structural variability can be observed for most proteins.

Availability: The results of the analysis of the SCOP alternative models, the estimates of coordinate uncertainty as well as the source code of the implementation are available in the STRuster web site: http://struster.bioinf.mpi-inf.mpg.de.

Contact: doming{at}mpi-sb.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Prof. Burkhard Rost

Received on June 12, 2007; revised on September 13, 2007; accepted on September 28, 2007

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