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

描述（由申请人提供）：结合特定蛋白质的小分子是控制生化过程的强大工具，关于小分子与蛋白质结合的信息可以帮助研究人员了解结合的物理基础，改进计算药物设计方法，建议其他化合物的生物活性机制，并且可能预测副作用。BindingDB通过提供web访问工具来浏览、查询、分析和下载这些蛋白质-小分子关联数据。在目前的资助期内，我们收集了约40,000个亲和度测量，丰富了网络界面，并与其他重要的生物信息学资源建立了联系。使用量急剧增长。我们现在建议通过以下目标将BindingDB提升到一个新的水平：极大地扩展BindingDB的定量绑定亲和力的核心数据集，通过自动化数据收集建立一个新的、更广泛的数据集，并在合作管理和数据共享方面与新的国际努力合作。通过创建化合物和蛋白质之间关系的创新概述，新的生物学和疾病导向浏览器以及亲和背景下分子结构的3D视图，增强web界面。创建与其他数据资源的新链接，并提供以编程方式使用BindingDB功能的工具。扩展和增强在线虚拟筛选工具的新方法和链接到大型复合目录。制作教育和教程材料。加强BindingDB的硬件和软件基础设施。通过BindingDB的科学顾问委员会、直接用户交互和研讨会响应社区指导。公共卫生相关性：该项目将扩展一个由美国国立卫生研究院资助的、可通过网络访问的数据库，该数据库包含了与疾病相关的蛋白质结合的类似药物的小分子的信息。这将有助于科学家设计新药，开发改进的药物设计计算机模型，并利用小分子探测生命系统并了解它们是如何工作的。

DESCRIPTION (provided by applicant): Small molecules that bind specific proteins are powerful tools for controlling biochemical processes, and information on the association of small molecules with proteins can help researchers understand the physical basis of binding, improve computational drug-design methods, suggest the bioactivity mechanisms of other compounds, and, potentially, predict side-effects. BindingDB enables these uses of protein-small molecule association data by providing web-accessible tools for browsing, querying, analyzing and downloading. During the current grant period, we have collected ~40,000 affinity measurements, enriched the web-interface, and linked to other important bioinformatics resources. Usage has grown dramatically. We now propose to take BindingDB to the next level through these aims: Greatly expand BindingDB's core dataset of quantitative binding affinities, establish a new, much broader dataset by automated data collection, and collaborate with new international efforts at cooperative curation and data sharing. Enhance the web interface by creating innovative overviews of relationships among compounds and proteins, new biology- and disease-oriented browsers, and 3D views of molecular structure in the context of affinity. Create new links with other data resources and provide tools for using BindingDB capabilities programmatically. Expand and enhance tools for on-line virtual screening with new methods and links to large compound catalogs. Create educational and tutorial materials. Strengthen BindingDB's hardware and software infrastructure. Respond to community guidance via BindingDB's Scientific Advisory Board, direct user interactions, and a workshop. PUBLIC HEALTH RELEVANCE: This project will expand an NIH-funded, web-accessible database of information about the binding of small, drug-like molecules to disease-related proteins. This will help scientists design new drugs, develop improved computer models for drug design, and use small molecules to probe living systems and learn how they work.