Identification rapide de familles protéiques par dominance

Mathilde Le Boudic-Jamin; Noël Malod-Dognin; Alexandre Cornu; Jacques Nicolas; Rumen Andonov

inria-00611457, version 1

Identification rapide de familles protéiques par dominance

Mathilde Le Boudic-Jamin ( Auteur à contacter de préférence )^b^, 1, Noël Malod-Dognin () ², Alexandre Cornu () ¹, Jacques Nicolas ()^a^, 1, Rumen Andonov ()^b^, 1

12th Annual Congress of the French National Society of Operations Research and Decision Science (ROADEF) 2 (2011) 791-792

Résumé : Structural comparison of proteins is a frequent and important operation in bioinformatics, giving precious information for determining the possible functions of proteins. Unfortunately, the corresponding optimization problems are often NP-Hard. Different analysis approaches exist: Most are based on the superimposition of residue coordinates (like VAST) or on the comparison of internal distances. The objective is to quickly identify and classify similar structures. We used the comparison tool A_purva, which is based on Contact Map Overlap (CMO), to classify protein structure coming from the CATH database. The obtained results show that A_purva was able to correctly classify 92% of the structures, and that introducing the notion of dominance drastically reduces the computational time needed for classifying the protein structures.

a – INRIA
b – Université de Rennes I
1 : SYMBIOSE (INRIA - IRISA)
CNRS : UMR6074 – INRIA – Institut National des Sciences Appliquées (INSA) - Rennes – Université de Rennes 1
2 : ABS (INRIA Sophia Antipolis)
INRIA

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http://hal.inria.fr/inria-00611457
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Contributeur : Noel Malod-Dognin <>
Soumis le : Mardi 26 Juillet 2011, 13:53:40
Dernière modification le : Vendredi 18 Novembre 2011, 17:02:03

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%% inria-00611457, version 1
%% http://hal.inria.fr/inria-00611457
@inproceedings{leboudicjamin:inria-00611457,
    hal_id = {inria-00611457},
    url = {http://hal.inria.fr/inria-00611457},
    title = {{Identification rapide de familles prot{\'e}iques par dominance}},
    author = {Le Boudic-Jamin, Mathilde and Malod-Dognin, No{\"e}l and Cornu, Alexandre and Nicolas, Jacques and Andonov, Rumen},
    abstract = {{Structural comparison of proteins is a frequent and important operation in bioinformatics, giving precious information for determining the possible functions of proteins. Unfortunately, the corresponding optimization problems are often NP-Hard. Different analysis approaches exist: Most are based on the superimposition of residue coordinates (like VAST) or on the comparison of internal distances. The objective is to quickly identify and classify similar structures. We used the comparison tool A\_purva, which is based on Contact Map Overlap (CMO), to classify protein structure coming from the CATH database. The obtained results show that A\_purva was able to correctly classify 92\% of the structures, and that introducing the notion of dominance drastically reduces the computational time needed for classifying the protein structures.}},
    keywords = {Protein comparison; alignment; branch and bounds; dominance},
    language = {Fran{\c c}ais},
    affiliation = {SYMBIOSE - INRIA - IRISA , ABS - INRIA Sophia Antipolis},
    booktitle = {{12th Annual Congress of the French National Society of Operations Research and Decision Science (ROADEF)}},
    pages = {791-792},
    address = {Saint-{\'E}tienne, France},
    organization = {{\'E}cole Nationale Sup{\'e}rieure des Mines de Saint-{\'E}tienne},
    volume = {2},
    note = {Publi{\'e} dans le douzi{\`e}me congr{\`e}s de la Soci{\'e}t{\'e} Fran{\c c}aise de Recherche Op{\'e}rationnelle et d'Aide {\`a} la D{\'e}cision (ROADEF 2011). RR-7696 RR-7696 },
    audience = {nationale },
    year = {2011},
    month = Mar,
    pdf = {http://hal.inria.fr/inria-00611457/PDF/RR-7696.pdf},
}

%F inria-00611457, version 1
%0 Conference Proceedings
%U http://hal.inria.fr/inria-00611457
%2 INFO:INFO_BI;SDV:BIBS
%T Identification rapide de familles protéiques par dominance
%A Le Boudic-Jamin, Mathilde
%A Malod-Dognin, Noël
%A Cornu, Alexandre
%A Nicolas, Jacques
%A Andonov, Rumen
%+ SYMBIOSE - INRIA - IRISA , ABS - INRIA Sophia Antipolis
%X Structural comparison of proteins is a frequent and important operation in bioinformatics, giving precious information for determining the possible functions of proteins. Unfortunately, the corresponding optimization problems are often NP-Hard. Different analysis approaches exist: Most are based on the superimposition of residue coordinates (like VAST) or on the comparison of internal distances. The objective is to quickly identify and classify similar structures. We used the comparison tool A_purva, which is based on Contact Map Overlap (CMO), to classify protein structure coming from the CATH database. The obtained results show that A_purva was able to correctly classify 92% of the structures, and that introducing the notion of dominance drastically reduces the computational time needed for classifying the protein structures.
%2 La comparaison de stuctures protéiques est une opération fréquente et importante dans le domaine de la bioinformatique. Elle apporte des informations aidant à la détermination des fonctions d'une protéine. Néanmoins, le problème sous-jacent est NP-complet. Différentes approches d'analyse existent: certaines basées sur la superposition de coordonnées (e.g. VAST) et d'autres sur les distances internes conservées dans les structures. L'objectif est donc d'identifier et de classer rapidement des structures similaires. Nous avons classé des structures de la base de données CATH avec un programme nommé A_purva qui utilise l'approche CMO (Conctact Map Overlap). Nous montrons que ce dernier a permis de prédire correctement la classification de 92% des structures soumises et que l'introduction de la notion de dominance a réduit considérablement les temps de classement des protéines.
%G Français
%8 2011-03-00
%2 nationale
%B 12th Annual Congress of the French National Society of Operations Research and Decision Science (ROADEF)
%2 Saint-Étienne
%2 France
%8 2011-03-02
%8 2011-03-04
%2 École Nationale Supérieure des Mines de Saint-Étienne
%V 2
%P 791-792
%K Protein comparison; alignment; branch and bounds; dominance
%Z Publié dans le douzième congrès de la Société Française de Recherche Opérationnelle et d'Aide à la Décision (ROADEF 2011).
%Z RR-7696
%2 8127

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