Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
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DOI：
10.1186/1475-2875-5-110
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发表时间：
2006-11-17
期刊：
影响因子：
3
通讯作者：
Maréchal E
中科院分区：
文献类型：
--
作者：
Birkholtz LM;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 AI;Maréchal E
组织和挖掘疟疾基因组和后基因组数据对于显著增加对其病原体生物学的了解是重要的，从长远来看，其动机是必须预测和确定新的生物目标和新药的特征。生物靶标是在根据恶性疟原虫基因组数据设计的生物空间中寻找的，但也使用了来自其他物种的数百万基因组数据。候选药物是在一个化学空间中寻找的，这个空间包含了储存在公共和私人化学实验室中的数百万个小分子。因此，数据管理应尽可能可靠和通用。在此背景下，对疟疾基因组和后基因组数据的组织和挖掘的五个方面进行了研究：1)蛋白质序列的比较，包括非典型疟疾序列的组成；2)分子系统发育的高通量重建；3)生物过程的表示，特别是代谢途径的表示；4)综合基因组数据、生物表示和药物治疗后X组实验获得的功能描述的通用方法；5)蛋白质结构的确定和预测及其与候选药物结构的分子对接。讨论了网格使能的化学基因组知识空间的最新进展。
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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影响因子：
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