dorsal/arxiv
View SchemaIntegration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
| Authors | L. -M. Birkholtz, O. Bastien, G. Wells, D. Grando, F. Joubert, V. Kasam, M. Zimmermann, P. Ortet, N. Jacq, S. Roy, M. Hoffmann-Apitius, V. Breton, A. I. Louw, E. Maréchal |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611053 |
| URL | https://arxiv.org/abs/q-bio/0611053 |
| DOI | 10.1186/1475-2875-5-110 |
| Journal | Malaria Journal 5 (2006) 1-24 |
Abstract
The organization and mining of malaria genomic and post-genomic data is highly motivated 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, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 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. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.
{
"annotation_id": "a0825a5d-cc77-4f95-82af-2a39f95bf4e4",
"date_created": "2026-03-02T18:01:35.793000Z",
"date_modified": "2026-03-02T18:01:35.793000Z",
"file_hash": "7a0906cc1901484a535037a5482f26dcbf8eeea0b9390c01e0532d0cc238f267",
"private": false,
"record": {
"abstract": "The organization and mining of malaria genomic and post-genomic data is\nhighly motivated by the necessity to predict and characterize new biological\ntargets and new drugs. Biological targets are sought in a biological space\ndesigned from the genomic data from Plasmodium falciparum, but using also the\nmillions of genomic data from other species. Drug candidates are sought in a\nchemical space containing the millions of small molecules stored in public and\nprivate chemolibraries. Data management should therefore be as reliable and\nversatile as possible. In this context, we examined five aspects of the\norganization and mining of malaria genomic and post-genomic data: 1) the\ncomparison of protein sequences including compositionally atypical malaria\nsequences, 2) the high throughput reconstruction of molecular phylogenies, 3)\nthe representation of biological processes particularly metabolic pathways, 4)\nthe versatile methods to integrate genomic data, biological representations and\nfunctional profiling obtained from X-omic experiments after drug treatments and\n5) the determination and prediction of protein structures and their molecular\ndocking with drug candidate structures. Progresses toward a grid-enabled\nchemogenomic knowledge space are discussed.",
"arxiv_id": "q-bio/0611053",
"authors": [
"L. -M. Birkholtz",
"O. Bastien",
"G. Wells",
"D. Grando",
"F. Joubert",
"V. Kasam",
"M. Zimmermann",
"P. Ortet",
"N. Jacq",
"S. Roy",
"M. Hoffmann-Apitius",
"V. Breton",
"A. I. Louw",
"E. Mar\u00e9chal"
],
"categories": [
"q-bio.QM",
"cs.DC",
"q-bio.GN"
],
"doi": "10.1186/1475-2875-5-110",
"journal_ref": "Malaria Journal 5 (2006) 1-24",
"title": "Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?",
"url": "https://arxiv.org/abs/q-bio/0611053"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "371f3b47-e47c-4ef1-8192-56e0bfd5e5c8",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}