BindingDB: Data and Tools for Drug Discovery, Chemical Biology and Systems Pharmacology

摘要 大多数药物是通过结合疾病相关蛋白质起作用的小有机分子。生物医学 研究产生了新的蛋白质的想法，这些蛋白质可以被新药靶向，成千上万的小分子 在工业界和学术界，合成并测试了分子结合这些靶向分子的能力。 proteins.化学生物学家还开发针对特定蛋白质的小分子，以阐明 途径和细胞机制。由此产生的蛋白质-配体相互作用数据流有许多用途 超越了产生它们的具体项目，例如测试和改进计算药物设计 技术，并产生生物活性化合物的作用机制的假设。但他们 几乎完全发表在科学文章和专利中，在这些文章和专利中， 系统地搜索浏览和检索BindingDB，第一个收集这些蛋白质的开放数据库- 小分子结合数据，并使它们可用于查询，下载和分析，为用户提供 在全球范围内，随时可以访问不断增长的数据集，目前有120万个数据用于50万个小分子 和成千上万的蛋白质。 在即将到来的资助期内，我们计划继续开展扩展BindingDB数据收集的核心活动 通过从其他在线资源中获取相关数据，并继续从新的 科学论文和专利。我们还将对BindingDB网站进行重大升级， 不那么杂乱的外观和新功能，如优化搜索结果的功能， BindingDB数据采集，并定制用户请求的数据下载内容。新功能 还将开发支持应用程序在新兴领域的系统药理学，通过注释 生物分子网络和途径中的蛋白质与来自BindingDB的小分子结合数据， 构建工具以定性地模拟具有小分子结合剂的干扰途径的影响。最后， 我们将通过各种渠道分享有关BindingDB的信息，并将与教育专家合作 开发和传播BindingDB的教学应用程序。

Abstract Most medications are small organic molecules which work by binding disease-related proteins. As biomedical research yields ideas for additional proteins which could be targeted by new drugs, thousands of small molecules are synthesized and tested, in both industry and academia, for their ability to bind these targeted proteins. Chemical biologists also develop small molecules targeted to specific proteins in order to elucidate pathways and cellular mechanisms. The resulting flow of protein-ligand interaction data have many uses well beyond the specific projects which generated them, such as testing and improve computational drug design technologies, and generating hypotheses for the mechanisms of action of bioactive compounds. However, they are published almost exclusively in scientific articles and patents, where they cannot be readily and systematically searched, browsed, and retrieved. BindingDB, the first open database to collect these protein- small molecule binding data and make them available for query, download, and analysis, provides users worldwide with ready access to a growing data collection, currently 1.2 million data for 500K small molecules and thousands of proteins. In the forthcoming grant period, we plan to continue the core activity of expanding BindingDB’s data collection by harvesting relevant data from other on-line resources and continuing in-house curation of data from new scientific articles and patents. We will also carry out major upgrades of the BindingDB web-site, providing a less cluttered look and new features, such as ones to refine search results, gain overviews of the large BindingDB data collection, and customize the content of data downloads requested by users. New capabilities will also be developed to support applications in the emerging field of systems pharmacology, by annotating the proteins in biomolecular networks and pathways with small molecule binding data from BindingDB and constructing tools to qualitatively model the effects of perturbing pathways with small molecule binders. Finally, we will share information about BindingDB through a variety of channels, and will work with education experts to develop and disseminate instructional applications of BindingDB.