THE STRUCTURE-FUNCTION LINKAGE DATABASE

结构-功能联系数据库

• 批准号: 8363588
• 负责人: PATRICIA CLEMENT BABBITT
• 金额: $ 2.79万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8363588
• 关键词: Amino Acid Sequence; Biochemistry; Chimera organism; Complex; Databases; Engineering; Enzymes; Funding; Future; Grant; Imagery; Informatics; Methods; Molecular; Names; National Center for Research Resources; Paper; Peptide Sequence Determination; Principal Investigator; Procedures; Publications; Reaction; Research; Research Infrastructure; Research Personnel; Resources; Source; Structure; Training; United States National Institutes of Health; Update; Work; biocomputing; cost; data management; interest; meetings; protein structure; symposium; tool; tool development; web interface; web-accessible

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The relationship between a given protein's structure and its molecular function can be quite complex, yet recently some of the fundamentals have been elucidated through the study of enzyme superfamilies. The Resource for Biocomputing, Visualization, and Informatics (RBVI) and the Babbitt lab are developing the SFLD (Structure-Function Linkage Database) database to leverage this information in a manner which will allow users to predict and engineer enzyme function. The SFLD is now a web-accessible database hosted by the RBVI. Currently supported are methods allowing users to search the database with a protein sequence, keyword (matching enzyme or reaction name), or with a reaction, substrate, product, or partial reaction as described by a SMILES string. Easy (i.e. single click) methods for users to visualize protein structures within the SFLD using Chimera are available. A web interface allowing curators of the SFLD to input and update information has recently be implemented, and is used by all current curators. A paper describing aspects of the SFLD was presented at the Pacific Symposium for Biocomputing in January 2005. The visibility of the SFLD continues to increase, aided by a very well-received, high-profile publication (Biochemistry, 2006 45(8):2545-55) and mutiple presentations at meetings. This increased visibility has drawn interest from multiple researchers outside UCSF who would like to use the SFLD as a data management tool for their own superfamily information. One focus of future work involves the development of tools and training procedures to aid these researchers in utilizing the SFLD for their own research purposes. The SFLD is available to the public at http://sfld.rbvi.ucsf.edu.

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 特定蛋白质的结构和其分子功能之间的关系可能非常复杂，但最近通过对酶超家族的研究已经阐明了一些基本原理。生物计算、可视化和信息学资源(RBVI)和巴比特实验室正在开发SFLD(结构功能链接数据库)数据库，以便以允许用户预测和设计酶功能的方式利用这些信息。 SFLD现在是一个可通过网络访问的数据库，由RBVI托管。当前支持的方法是允许用户用蛋白质序列、关键字(匹配的酶或反应名称)、或如微笑串所描述的反应、底物、产物或部分反应来搜索数据库。用户可以使用简单(即点击)方法使用嵌合体可视化SFLD内的蛋白质结构。 最近实施了一个网络界面，允许SFLD的馆长输入和更新信息，所有现任馆长都在使用该界面。 2005年1月在太平洋生物计算专题讨论会上提交了一篇介绍SFLD各方面内容的论文。在广受欢迎的高知名度出版物(生物化学，2006年45(8)：2545-55)和在会议上的多次发言的帮助下，SFLD的知名度继续提高。这种提高的可见性吸引了加州大学旧金山分校以外的多名研究人员的兴趣，他们希望将SFLD用作自己的超级家庭信息的数据管理工具。未来工作的一个重点是开发工具和培训程序，以帮助这些研究人员将SFLD用于他们自己的研究目的。 公众可在http://sfld.rbvi.ucsf.edu.上查阅《可持续发展报告》。