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Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

Lyn-Marie Birkholtz1 email, Olivier Bastien2 email, Gordon Wells3 email, Delphine Grando4 email, Fourie Joubert3 email, Vinod Kasam5 email, Marc Zimmermann6 email, Philippe Ortet7 email, Nicolas Jacq5 email, Nadia Saïdani4,8 email, Sylvaine Roy9 email, Martin Hofmann-Apitius6 email, Vincent Breton5 email, Abraham I Louw1 email and Eric Maréchal4 email

Department of Biochemistry and African Centre for Gene Technologies, Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002, Pretoria, South Africa

UMR 5163 CNRS-Université Joseph Fourier, Laboratoire Adaptation et Pathogénie des Microorganismes, Institut Jean Roget, 38700, La Tronche, France

Bioinformatics and Computational Biology Unit, Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002, Pretoria, South Africa

UMR 5168 CNRS-CEA-INRA-Université Joseph Fourier, Département Réponse et Dynamique Cellulaires; CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cedex 09, France

Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS-IN2P3, Campus des Cézeaux, 63177 Aubière Cedex, France

Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53754 Sankt Augustin, Germany

Département d'Ecophysiologie Végétale et de Microbiologie; CEA Cadarache, 13108 Saint Paul-lez-Durance, France

UMR 5539 CNRS-Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier cedex 05, France

Laboratoire de Biologie, Informatique et Mathématiques; Département Réponse et Dynamique Cellulaires; CEA Grenoble, 17 rue des Martyrs, F-38054, Grenoble cedex 09, France

author email corresponding author email

Malaria Journal 2006, 5:110doi:10.1186/1475-2875-5-110

Published: 17 November 2006

Abstract

The organization and mining of malaria genomic and post-genomic data is important to significantly increase the knowledge of the biology of its causative agents, and is motivated, on a longer term, by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should, therefore, be as reliable and versatile as possible. In this context, five aspects of the organization and mining of malaria genomic and post-genomic data were examined: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes, particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Recent progress towards a grid-enabled chemogenomic knowledge space is discussed.


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