title: Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
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.
authors.affiliation: Department of Biochemistry and African Centre for Gene Technologies, Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002, Pretoria, South Africa. lynmarie.birkholtz@up.ac.za <lynmarie.birkholtz@up.ac.za>
authors.forename: Lyn-Marie
authors.initials: LM
authors.lastname: Birkholtz
authors.forename: Olivier
authors.initials: O
authors.lastname: Bastien
authors.forename: Gordon
authors.initials: G
authors.lastname: Wells
authors.forename: Delphine
authors.initials: D
authors.lastname: Grando
authors.forename: Fourie
authors.initials: F
authors.lastname: Joubert
authors.forename: Vinod
authors.initials: V
authors.lastname: Kasam
authors.forename: Marc
authors.initials: M
authors.lastname: Zimmermann
authors.forename: Philippe
authors.initials: P
authors.lastname: Ortet
authors.forename: Nicolas
authors.initials: N
authors.lastname: Jacq
authors.forename: Nadia
authors.initials: N
authors.lastname: Saïdani
authors.forename: Sylvaine
authors.initials: S
authors.lastname: Roy
authors.forename: Martin
authors.initials: M
authors.lastname: Hofmann-Apitius
authors.forename: Vincent
authors.initials: V
authors.lastname: Breton
authors.forename: Abraham I
authors.initials: AI
authors.lastname: Louw
authors.forename: Eric
authors.initials: E
authors.lastname: Maréchal
mesh_terms: D000818:Animals; D000962:Antimalarials / Q000494:pharmacology; D018503:Genome, Protozoan; D008024:Ligands; D010802:Phylogeny; D010961:Plasmodium / Q000737:chemistry / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D015800:Protozoan Proteins / Q000737:chemistry
chemical_list: D000962:Antimalarials; D008024:Ligands; D015800:Protozoan Proteins