PubChem 作为一个公共的药物发现资源。
PubChem as a public resource for drug discovery.
机构信息
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
出版信息
Drug Discov Today. 2010 Dec;15(23-24):1052-7. doi: 10.1016/j.drudis.2010.10.003. Epub 2010 Oct 21.
Abstract
PubChem is a public repository of small molecules and their biological properties. Currently, it contains more than 25 million unique chemical structures and 90 million bioactivity outcomes associated with several thousand macromolecular targets. To address the potential utility of this public resource for drug discovery, we systematically summarized the protein targets in PubChem by function, 3D structure and biological pathway. Moreover, we analyzed the potency, selectivity and promiscuity of the bioactive compounds identified for these biological targets, including the chemical probes generated by the NIH Molecular Libraries Program. As a public resource, PubChem lowers the barrier for researchers to advance the development of chemical tools for modulating biological processes and drug candidates for disease treatments.
摘要
PubChem 是一个小分子及其生物特性的公共数据库。目前，它包含超过 2500 万个独特的化学结构和 9000 万个与数千个大分子靶标相关的生物活性结果。为了探索这个公共资源在药物发现方面的潜在应用，我们系统地按照功能、3D 结构和生物途径对 PubChem 中的蛋白质靶标进行了总结。此外，我们还分析了针对这些生物靶标鉴定的生物活性化合物的效力、选择性和广谱性，包括 NIH 分子文库计划生成的化学探针。作为一个公共资源，PubChem 降低了研究人员开发用于调节生物过程的化学工具和用于治疗疾病的候选药物的门槛。
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1
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2
Probing the probes: fitness factors for small molecule tools.探索探针：小分子工具的适用性因素
Chem Biol. 2010 Jun 25;17(6):561-77. doi: 10.1016/j.chembiol.2010.05.013.
3
The art of the chemical probe.化学探针的技术
Nat Chem Biol. 2010 Mar;6(3):159-161. doi: 10.1038/nchembio.296.
4
An overview of the PubChem BioAssay resource.PubChem 生物测定资源概述。
Nucleic Acids Res. 2010 Jan;38(Database issue):D255-66. doi: 10.1093/nar/gkp965. Epub 2009 Nov 19.
5
KEGG for representation and analysis of molecular networks involving diseases and drugs.KEGG 用于表示和分析涉及疾病和药物的分子网络。
Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60. doi: 10.1093/nar/gkp896. Epub 2009 Oct 30.
6
Novel trends in high-throughput screening.高通量筛选的新趋势。
Curr Opin Pharmacol. 2009 Oct;9(5):580-8. doi: 10.1016/j.coph.2009.08.004. Epub 2009 Sep 21.
7
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J Chem Inf Model. 2009 Sep;49(9):2044-55. doi: 10.1021/ci9001876.
8
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9
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10
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