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

: Birkholtz, L.-M.; Bastien, O.; Wells, G.; Grando, D.; Joubert, F.; Kasam, V.; Zimmermann, M.; Ortet, P.; Jacq, N.; Saïdani, N.; Roy, S.; Hofmann-Apitius, M.; Breton, V.; Louw, A.I.; Maréchal, E.

Fulltext urn:nbn:de:0011-n-574927 (1.0 MByte PDF)
MD5 Fingerprint: 5c5a958535e2e2906e8f58c5e177f4c2
Created on: 25.05.2007

Malaria journal. Online journal 5 (2006), Art. 110, 24 pp.
ISSN: 1475-2875
Journal Article, Electronic Publication
Fraunhofer SCAI ()

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.