Comparing Protein 3D Structures Using A_purva

Noël Malod-Dognin 1, * Nicola Yanev 2 Rumen Andonov 3
* Corresponding author
1 ABS - Algorithms, Biology, Structure
CRISAM - Inria Sophia Antipolis - Méditerranée
3 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : Structural similarity between proteins provides significant insights about their functions. Maximum Contact Map Overlap maximization (CMO) received sustained attention during the past decade and can be considered today as a credible protein structure measure. We present here A_purva, an exact CMO solver that is both efficient (notably faster than the previous exact algorithms), and reliable (providing accurate upper and lower bounds of the solution). These properties make it applicable for large-scale protein comparison and classification. Availability: http://apurva.genouest.org Contact: support@genouest.org Supplementary information: A_purva's user manual, as well as many examples of protein contact maps can be found on A_purva's web-page.
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Noël Malod-Dognin, Nicola Yanev, Rumen Andonov. Comparing Protein 3D Structures Using A_purva. [Research Report] RR-7464, INRIA. 2010, pp.9. ⟨inria-00539939⟩

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