Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
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Section: New Results

Multiple Flexible Protein Structure Alignments

Comparing two or more proteins by optimally aligning and superposing their backbone structures provides a way to detect evolutionary relationships between proteins that cannot be detected by comparing only their primary amino-acid sequences. The latest version of our “Kpax” protein structure alignment algorithm can flexibly align pairs of structures that cannot be completely superposed by a single rigid-body transformation, and can calculate multiple alignments of several similar structures flexibly [9]. In collaboration with Alain Hein of the INRA lab “Agronomie et Environnement”, we used Kpax to help study the structures of various “Cyp450” enzymes in plants [21]. In collaboration with Emmanuel Levy of the Weizmann Institute, we used Kpax to superpose and compare all of the symmetrical protein complexes in the Protein Databank in order to verify or remediate their quaternary structure annotations. A manuscript describing this work has been published in Nature Methods [16].