你所要了解的32个化学数据库.doc

。16 十 11 你所要了解的32个免费化学数据库来自Rich Apodaca的Blog，简单翻译了一下，注明来源后欢迎转载。1. PubChem- 免费化学数据库的始祖。可以通过多种查询条件搜索超过八百万种化合物。虽然有部分PubChem记录通过MeSH链接到了原始文献中，但是大多数记录并没有链接到相应的原始文献。 不过PubChem的初衷并不是文献检索。PubChem很大程度上参与到了世界最大的在线分子数据表集合中，本列表种的其他数据库都将他们的条目交叉引用到了PubChem中。PubChem的整个数据库都可以通过FTP下载。PubChem是CAS Registry所碰到的真正对手。2. ZINC- 一个免费的商业数据库，包括虚拟筛选可用的化合物。可以通过结构、IUPAC名称、InChl和一系列运算出的属性，检索超过460万种化合物。对于非商业用途，你可以下载全部或者部分ZINC数据库在本地使用。3. eMolecules-Google分子数据。通过简单的接口和超快的搜索引擎，eMolecules 通过其他信息来源补充了PubChem的数据。尽管eMolecules的重点是可以通过商业手段获得的数据，但是只有部分分子可以指向到供应商的在线目录中。eMolecules种的大多数条目都是链接到PubChem中的，因此我觉得现在eMolecules 的用处并不是很大。如果你想起了一个叫做Chmoogle的东西，那其实就是eMolecules。(别把它和Google弄混了)。4. CHEBI- 一个免费的小分子化合物在线词典。CHEBI的数据主要来自两个来源: Integrated Relational Enzyme Database of the EBIhythe Kyoto Encyclopedia of Genes and Genomes。 你可以找出分子在什么情况下和哪些蛋白质有关。该数据库同时也提供与CAS注册号、Beilstein注册号和Gmelin注册号的交叉链接。5. NIST Chemistry WebBook- 提供大多数有机化合物的物理数据 (包括热化学、 热物理学和热力学信息) 。可以通过分子式、结构、CAS号和IUPAC名称搜索。6. BioCyc- 搜集了包含酶基质、酶产品、酶抑制剂、酶激活剂在内的3500种化合物。在接受一个授权协议的情况下，整个数据库都可以按照Chemical Markup Language格式免费下载。7. ChemExper- 查找你所需要的化学品的供应商。可以通过结构、名称、分子式和CAS号进行检索。找到化合物之后，你可以向一个或者多个供应商进行询价。我没有实际尝试过，不过听起来主义不错。8. Compendium of Pesticide Common Names- 超过1100常用农药。化合物是需要通过浏览索引页面而不能通过搜索查找。 Each entry lists, among other pieces of information, a chemical structure and sub-classifications (repellents, antifeedants, synergists, etc.).9. NMRShiftDB- 提供有机分子结构及其核磁共振（ NMR ）的化学位移。nmrshiftdb含有超过22000有机化合物的化学位移数据和19000个谱图。你可以通过结构、化学位移和核（nucleus?what?）检索记录。NMRShiftDB完全开放，它可以通过编程方式访问，并且运行在线数据库的软件源代码也可以免费下载。人用户可以提交自己的谱图或者位移数据，以供别人审阅或者列入数据库中。10. Chemical Structure Lookup Service(CSLS)- 一个化学结构目录。如果你用过Metacrawler, 那么你应该了解SCLS的原理，即从多个免费化学数据库种查找数据。你可以通过IUPAC名称、InChI、结构、SMILES和一系列的分子特征查找超过两千七百万种化合物。你的搜索结构种会包括含有你所要搜索的分子的数据库的链接。用户界面不止是不好看的问题了，简直是太烂了。如果你不在意用户界面的话，CSLS可能是这个列表中最有用的服务之一。11. DrugBank- Combines detailed drug data with comprehensive drug target information. Search over 4,300 drugs by trade name, SMILES, and InChI. Each record contains information on target of action, therapeutic indication, medications the drug is an ingredient of, and trade names. Searches can be limited to only approved drugs or experimental drugs. Both the concept and interface to this service are well thought-out.Note: this service was unavailable as of Jan 19, 200712. Wikipedia- Wikipedia? Yes, Wikipedia. Wikipedia offers several kinds of chemical information produced by a knowledgeable, all-volunteer army. Looking for information on organic compounds? Considerthis datasheet on morphineas an example. For those interested in synthesis, Wikipedia is increasingly being used to collaboratively authorshort reviews on the topic. Search capabilities are currently limited to text and dont appear to work with IUPAC names or CAS numbers. Where this quintessentialdisruptive technologyand its offspring end up taking chemical publishing is unclear, but the ride will be spectacular.13. ChemDB- A chemical database is but one of the services offered by this site. Search over 4.1 million compounds by structure, or various calculated properties. ChemDB also offers a variety of free online cheminformatics tools such as Babel file format conversion, SMILES depict, and molecular property calculation. Read more about ChemDB inthisBioinformaticspaper.14. ChemBank- Structure search over 36,000 original biological assays of small molecules collected by HarvardsInstitute of Chemistry and Cell Biology(ICCB). Many of the data contained in ChemBank have never been published, making this database particularly valuable.15. National Institute of Allergy and Infectious Diseases Database- Structure search hundreds of thousands of screening datapoints collected by the NIAID in its HIV, Opportunistic Infection, and TB programs.16. National Toxicology Program- Seach by name for compounds listed in the NTP database. Returns detailed internal reports and links to the primary literature.17. NIST Chemical Kinetics Database- Search by reagent or product name or formula for gas phase rate constants collected from the primary literature.18. Computational Chemstry Comparison and Benchmark Database- Search by formula for over 600 gas phase atom and molecule physical chemistry data obtained experimentally and by computation.19. IUPAC-NIST Solubility Data Series- Search by name or CAS number through over 67,000 solubility measurements. Data were comprehensively compiled from over 1,800 references in primary literature.20. SOLV-DB- Search over 200 common solvents by name, CAS number, or chemical formula physical. Available data include boiling point, water solubility, viscosity, octanol-water partition constant, flash point, and a variety of other properties.21. NIMH Pyschoactive Drug Screening Program KiDatabase- Search over 44,000 Kideterminations culled from the literature. Although this database appears to have no structure search capability, this is listed as a Future Enhancement. This is a perfect example of a very useful service that could do with a major user interface redesign. There also appears to be another (defunct) service by the same name, but adifferent URL.22. Kyoto Encyclopedia of Genes and Genomes (KEGG)- A Japanese counterpart to PubChem/PubMed. One of the most interesting services on this list, KEGG consists of four interconnected databases: KEGG Pathway; KEGG genes; KEGG Brite; and KEGG Ligand. KEGG Ligand contains over 14,000 compounds searchable by name, and crosslinked to over 45,000 biological pathways. The KEGG Ligand database can be searched by structure throughKegDraw, a 2-D structure editor written in Java. With some minor configuration on my Linux system, I was able to perform some basic substructure searches using KegDraw. Your mileage may vary. A nice overview of KEGG is available in arecent article. The contents of KEGG can bedownloaded by anonymous ftpfor academic use.23. BRENDA- Search over 40,000 structures as substrates, products, cofactors, or inhibitors for enzymes. Although my search was able to find compounds by substructure, I was not able to view any links to the results. Your mileage may vary.24. Biochemical Pathways Database- Structure search over 1,100 small molecules as participants in biochemical pathways. A potentially useful service, but currently too slow to fully evaluate. A structure search for naphthalene hung for five minutes before I terminated it without success.25. ChemMine- Search by structure for compounds collected from a variety of open databases. View assay results in annotated biological experiments. I find the layout and organization of this service annoyingly confusing, but the underlying information appears to be useful nevertheless. Behind the scenes, ChemMine uses two open source cheminformatics libraries:Open BabelandJOELib. For a more detailed view of ChemMine, see therecent article.26. Organic Syntheses- Search by structure through the entire contents of synthetic organic chemistrys flagship resource. Substructure search requires Chime, so if you run Linux, or for some other reason cant install the plugin, youll be out of luck.27. WebReactions- Structure search organic reactions in four databases containing a total of over 391,000 reactions. Each reaction hit is linked to the primary literature through a bibliographical reference. Although the interface takes some getting used to, WebReactions may make a worthy companion to the traditional SciFinder search.28. Spectral Database for Organic Compounds (SDBS)- Search by name, molecular formula, molecular weight range, or CAS number through over 14,000 full1H NMR spectra, 12,000 full13C spectra, and 50,000 full FT-IR spectra collected from over 32,000 compounds.29. BindingDB- Structure search over 24,000 Kiand IC50measurements from over 10,000 molecules. Data is collected from, and cross-referenced to, the primary literature. I was unable to determine how to submit a substructure search through the Marvin applet on my Linux system (there is no Search button, for example). A text search for naphthalene, for example, showed some impressive potential for this database. Anyone can currently contribute to BindingDB, one of the few databases on this list to have such a policy.30. PDBBind- Browse over 2,700 complexes of small molecules ligands with proteins found in the Protein Databank. Structure searching requires a license. 3-D rendering comes courtesy of the ever-popul