Chemical Biology Information Resources

化学生物学信息资源

• 批准号: 7735086
• 负责人: stephen h bryant
• 金额: $ 353.48万
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7735086
• 关键词: Affect; Amino Acid Sequence; Award; Biological; Biological Assay; Biology; Books; Chemical Structure; Chemicals; Collection; Contrast Media; Daily; Data; Databases; Deposition; Genes; Grant; Growth; Hour; Image; Individual; Informatics; Information Resources; Information Services; Link; Literature; MeSH Thesaurus; Modeling; Molecular Bank; Names; Numbers; Object Attachment; Peptide Sequence Determination; Pharmaceutical Preparations; Process; Proteins; Protocols documentation; PubMed; Records; Reporting; Resources; Schedule; Score; Screening procedure; Sorting - Cell Movement; Source; Standardization; Structure; System; Testing; Toxicology; United States National Institutes of Health; Update; base; chemical group; conformer; crosslink; day; improved; indexing; molecular imaging; programs; protein structure; repository; research study; tautomer; three dimensional structure; tool

PubChem provides a public repository of chemical-structure records contributed by more than 80 organizations. Processing is automated, allowing PubChem's substance database to grow to over 40 million records in less than 5 years. A critical aspect of chemical-structure processing is standardization of valence-bond models, to provide the unique tautomer and/or resonance form stored in PubChem's compound datbase. Standardization enables cross-linking of deposited records that represent identical chemicals and calculation of accurate comparison scores to detect chemicals with similar though not identical structures. PubChem's chemical structure databases can be searched by chemical name or structure and can display results as Entrez "docsum" lists, structure similarity diagrams, or detailed "summary" records that include biological activity information. An informatics project undertaken this year has enabled rapid daily update of PubChem's chemical structure database. Depositors often provide millions of new or modified records per day, such that loading of deposited and standardized structures may take many minutes or hours. The redesigned system carefully schedules updates with replication and backup of the multiple PubChem database servers, as necessary to provide uninteruppted information services to users. Another informatics project still in progress calculates theoretical three dimensional structures of compounds in PubChem. These will be used to calculate structural similarities based on three dimensional conformer similarity, and in particular to PubChem analysis tools that cluster chemical structures and their biological activities in multiple PubChem Bioassay records. PubChem's Bioassay database is a repository for the results of chemical biology screening experiemnts, largely provided by grantees of the NIH Molecular Libraries roadmap program. The number of bioassay records has grown rapidly this year to over 1,100 records containing in total over 30 million tests of specific biological activities of individual chemical compounds. Bioassay records contain a description of the experimental protocol and are carefully curated to assure clarity of the experimental readouts provided in the data table associated with each record. Bioassay records are automatically neighbored to one another when they report one or more of the same chemicals as biologically active and/or when they link to target proteins or genes sequence-similar to one another. New Molecular Libraries grants were awarded in September 2008 and the growth of PubChem's Bioassay database is expected to continue. An important informatics project undertaken this year has been to provide simpler links from compounds to information on their biolgoical activity. A tool shown at the top of every Entrez "docsum" list of compounds provides "Bioactivity Analysis", a list of PubChem Bioassay records where one or more of the chemicals was tested, so sorted as to place experiments with the greatest number of bioactives at the top of the list. From the "Bioactivity Analysis" page a further link is provided to "Structure Activity", presenting an informative display of chemicals grouped by structural similarity and bioassays grouped by active-compound overlap or target sequence similarity. Another informatics project still underway improves NLM drug and toxicology information in compound "summary" and Entrez "docsum" displays. The NIH Molecular Libraries roadmap project has supported another database in addition to PubChem, the Molecular Imaging and Contrast Agent Database or MICAD, presented as one of the collections in the Entrez "Books" database. MICAD is a collection of regularly-formated review articles, each describing an imaging agent with links to PubChem records for chemical structure and PubMed articles cited in the review. Curators on the MICAD team author the reviews and create PubChem records needed for each. The total number of MICAD review article supassed 500 in summer of 2008.

PubChem 提供了由 80 多个组织贡献的化学结构记录的公共存储库。处理是自动化的，使得 PubChem 的物质数据库在不到 5 年内增长到超过 4000 万条记录。化学结构处理的一个关键方面是价键模型的标准化，以提供存储在 PubChem 化合物数据库中的独特互变异构体和/或共振形式。标准化可以交联代表相同化学品的存放记录，并计算准确的比较分数，以检测具有相似但不相同结构的化学品。 PubChem 的化学结构数据库可以按化学名称或结构进行搜索，并且可以将结果显示为 Entrez“文档和”列表、结构相似性图或包含生物活性信息的详细“摘要”记录。 今年开展的一个信息学项目实现了 PubChem 化学结构数据库的每日快速更新。存款人通常每天提供数百万条新的或修改的记录，因此加载存款和标准化结构可能需要数分钟或数小时。重新设计的系统根据需要仔细安排更新，复制和备份多个 PubChem 数据库服务器，以便为用户提供不间断的信息服务。另一个仍在进行中的信息学项目计算 PubChem 中化合物的理论三维结构。这些将用于基于三维构象异构体相似性计算结构相似性，特别是用于将多个 PubChem 生物测定记录中的化学结构及其生物活性聚类的 PubChem 分析工具。 PubChem 的生物测定数据库是化学生物学筛选实验结果的存储库，主要由 NIH 分子图书馆路线图计划的受资助者提供。今年生物测定记录的数量迅速增长，达到 1,100 多条记录，总共包含超过 3,000 万次对单个化合物的特定生物活性的测试。生物测定记录包含实验方案的描述，并经过精心策划，以确保与每条记录相关的数据表中提供的实验读数清晰。当生物测定记录报告一种或多种具有生物活性的相同化学物质和/或当它们与彼此相似的目标蛋白质或基因序列连接时，生物测定记录会自动彼此相邻。新的分子图书馆拨款于 2008 年 9 月授予，PubChem 的生物测定数据库预计将继续增长。 今年开展的一个重要的信息学项目是提供化合物与其生物活性信息之间的更简单的链接。每个 Entrez“docum”化合物列表顶部显示的工具提供“生物活性分析”，这是一个 PubChem 生物测定记录列表，其中测试了一种或多种化学物质，并进行排序，以便将具有最大数量生物活性的实验放在列表顶部。从“生物活性分析”页面，提供了指向“结构活性”的进一步链接，显示了按结构相似性分组的化学物质和按活性化合物重叠或目标序列相似性分组的生物测定的信息显示。另一个信息学项目仍在进行中，旨在改进化合物“摘要”和 Entrez“文档汇总”显示中的 NLM 药物和毒理学信息。 NIH 分子图书馆路线图项目还支持除 PubChem 之外的另一个数据库，即分子成像和造影剂数据库或 MICAD，作为 Entrez“书籍”数据库中的集合之一。 MICAD 是定期格式的评论文章的集合，每篇文章都描述了一种显像剂，并带有指向化学结构的 PubChem 记录和评论中引用的 PubMed 文章的链接。 MICAD 团队的策展人撰写评论并创建每个评论所需的 PubChem 记录。 2008年夏季，MICAD综述文章总数突破500篇。

项目成果

NIH MICAD initiative and guest author program opportunities.

NIH MICAD 倡议和客座作者项目机会。

• 发表时间: 2007
• 期刊: Journal of nuclear medicine : official publication, Society of Nuclear Medicine
• 作者: Cheng,KennethT;Menkens,Anne;Bryant,Steve;Sullivan,DanielC
• 通讯作者: Sullivan,DanielC

Fast 3D shape screening of large chemical databases through alignment-recycling.

• DOI: 10.1186/1752-153x-1-12
• 发表时间: 2007-06-06
• 期刊: Chemistry Central journal
• 作者: Fontaine F;Bolton E;Borodina Y;Bryant SH
• 通讯作者: Bryant SH