Recent Advances in Solving the Protein Threading Problem

Rumen Andonov; Guillaume Collet; Jean-François Gibrat; Antoine Marin; Vincent Poirriez; Nicola Yanev

inria-00165274, version 2

Recent Advances in Solving the Protein Threading Problem

Rumen Andonov ()^a^, 1, Guillaume Collet^a^, 1, Jean-François Gibrat^b^, 2, Antoine Marin^b^, 2, Vincent Poirriez^c^, 3, Nicola Yanev ()^d^, 1

N° RR-6253 (2007)

Résumé : The fold recognition methods are promissing tools for capturing the structure of a protein by its amino acid residues sequence but their use is still restricted by the needs of huge computational resources and suitable efficient algorithms as well. In the recent version of FROST (Fold Recognition Oriented Search Tool) package the most efficient algorithm for solving the Protein Threading Problem (PTP) is implemented due to the strong collaboration between the SYMBIOSE group in IRISA and MIG in Jouy-en-Josas. In this paper, we present the diverse components of FROST, emphasizing on the recent advances in formulating and solving new versions of the PTP and on the way of solving on a computer cluster a million of instances in a easonable time.

a – Université Rennes I
b – INRA
c – Université de Valenciennes et du Hainaut-Cambresis
d – Sofia University
1 : SYMBIOSE (INRIA - IRISA)
CNRS : UMR6074 – INRIA – Institut National des Sciences Appliquées (INSA) - Rennes – Université de Rennes 1
2 : Unité Mathématique Informatique et Génome (MIG)
Institut national de la recherche agronomique (INRA)
3 : Laboratoire d'automatique et de mécanique industrielles et humaines (LAMIH)
CNRS : UMR8530 – Université de Valenciennes et du Hainaut-Cambresis

inria-00165274, version 2
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Contributeur : Rapport De Recherche Inria <>
Soumis le : Lundi 30 Juillet 2007, 14:36:00
Dernière modification le : Lundi 30 Juillet 2007, 14:45:39

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