Protein Structure

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A-purva: Contact Map Overlap solver

Description 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. Reference 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 …

MD-jeep: Distance Geometry solver

Description MD-jeep is a software tool for solving distance geometry problems. It is able to solve a subclass of instances of the problem for which a discrete reformulation can be supplied. We refer to this subclass of instances as the Discretizable Molecular Distance Geometry Problem (DMDGP). We employ a Branch & Prune (BP) algorithm for …