Section: Software and Platforms

3D Protein structures

Participants : Rumen Andonov, Guillaume Chapuis, Mathilde Le Boudic-Jamin, Antonio Mucherino.

• CSA and DALIX CSA (Comparative Structural Alignment) is a webserver for computing and comparing protein structure alignments. CSA is able to compute score-optimal alignments with respect to various inter-residue distance-based scoring schemes. [contact: R. Andonov] http://csa.project.cwi.nl/

• A_purva 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. [contact: R. Andonov] http://mobyle.genouest.org/cgi-bin/Mobyle/portal.py?forms:A_Purva

• MD-Jeep 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 the solution of DMDGPs. [contact: A. Mucherino] http://www.antoniomucherino.it/en/mdjeep.php