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A-purva: Contact Map Overlap solver


A_purva is a Contact Map Overlap maximization (CMO) solver. Given two protein structures represented by two contact maps, A_purva computes the amino-acid alignment which maximize the number of common contacts.


N. Malod-Dognin, N. Yanev. R. Andonov, Comparing Protein 3D Structures Using A_purva, INTIA Research Report RR 7464, 2010

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.

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