BindingDB: A Tool for Drug Discovery, Modeling and Chemical and Systems Biology

描述（由申请人提供）：大多数药物通过结合特定的疾病相关蛋白起作用；靶向结合特定蛋白质的分子也被用作化学探针来阐明途径和生物分子机制。多年的药物发现和化学生物学研究已经产生了大量的分子识别数据，这些数据不仅对药物发现和化学生物学有价值，而且对系统药理学和药物基因组学等新兴领域也有价值。然而，多年来，这些数据很难获取和使用，因为它们几乎完全以专利和科学文献的形式发表，因此无法以机器可读的形式提供。我们的BindingDB数据库于2000年末上线，它是第一个从科学文献中收集这些绑定数据的公共数据库，并在Web上提供这些数据以供查询、下载和分析。如今，BindingDB的网站每月提供约8000名访问者，随时可以访问34万种不同的药物样小分子和6400种蛋白质的近80万份结合数据，其中大多数是候选药物靶点。美国国立卫生研究院（NIH）对转化研究的高度关注以及许多大学对药物发现的兴趣日益浓厚，增强了BindingDB的重要性。在即将到来的资助期内，我们计划进一步提高BindingDB对生物医学研究界的价值。BindingDB的核心工作将是继续扩大BindingDB的数据收集，通过合作从科学文献中整理蛋白质-小分子结合数据，启动专利数据整理，并扩大我们的范围，包括选定的生物制药。我们将进一步开发和部署用于访问、查看、分析和应用BindingDB中包含的数据的创新工具。例如，我们的目标是创建高级浏览器，允许用户在BindingDB的数据海洋中导航；将BindingDB的数据和功能与新兴的工作流系统连接起来，进行信息分析和可视化；并扩展BindingDB的工具，以支持系统药理学和药物基因组学。

DESCRIPTION (provided by applicant): Most drugs work by binding specific, disease-related proteins; and molecules targeted to bind specific proteins are also used as chemical probes to elucidate pathways and biomolecular mechanisms. Years of drug discovery and chemical biology research have generated a large body of molecular recognition data, which are of value not only for drug discovery and chemical biology, but also in the emerging fields of systems pharmacology and pharmacogenomics. However, for many years, these data were hard to access and use because they are published almost exclusively in patents and the scientific literature, and hence have not been available in machine-readable form. Our BindingDB database came on line in late 2000 as the first public database collecting a broad set of these binding data from the scientific literature and offering it on the Web for query, download, and analysis. Today, BindingDB's web-site provides about 8,000 visitors a month with ready access to nearly 800,000 binding data for 340,000 different drug-like small molecules and 6,400 proteins, most of them candidate drug-targets. BindingDB's significance is enhanced by the NIH's intensifying focus on translational research and a growing interest in drug- discovery at many universities. In the coming grant period, we plan to further improve BindingDB's value to the biomedical research community. A central effort will be to continue expanding BindingDB's data collection, by collaboratively curating protein-small molecule binding data from the scientifi literature, initiating data curation from patents, and broadening our scope to include selected biopharmaceuticals. We will furthermore develop and deploy innovative tools for accessing, viewing, analyzing and applying the data contained within BindingDB. For example, we aim to create high-level browsers that will allow users to navigate the sea of data within BindingDB; connect BindingDB's data and functionalities with emerging workflow systems for information analysis and visualization; and expand BindingDB's tools in support of systems pharmacology and pharmacogenomics.