Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
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.
Birkholtz
Lyn-Marie
LM
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>
Bastien
Olivier
O
Wells
Gordon
G
Grando
Delphine
D
Joubert
Fourie
F
Kasam
Vinod
V
Zimmermann
Marc
M
Ortet
Philippe
P
Jacq
Nicolas
N
Saïdani
Nadia
N
Roy
Sylvaine
S
Hofmann-Apitius
Martin
M
Breton
Vincent
V
Louw
Abraham I
AI
Maréchal
Eric
E
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
D000962:Antimalarials; D008024:Ligands; D015800:Protozoan Proteins