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.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 给定蛋白质的结构及其分子功能之间的关系可能很复杂，但是最近通过研究酶超家族的研究已经阐明了一些基本面。 生物计算，可视化和信息学（RBVI）和BABBITT实验室的资源正在开发SFLD（结构函数链接数据库数据库）数据库，以以允许用户预测和工程酶功能的方式利用此信息。 SFLD现在是由RBVI托管的可访问的数据库。当前支持的方法是允许用户使用蛋白质序列，关键字（匹配酶或反应名称）或反应，底物，产物或部分反应的方法搜索数据库。可以使用Chimera在SFLD中可视化SFLD中可视化蛋白质结构的简单方法（即单击）方法。 最近已经实现了一个允许SFLD策展人输入和更新信息的Web界面，并被所有当前策展人使用。 一篇描述SFLD方面的论文在2005年1月的太平洋研讨会上发表了生物计算。SFLD的可见性不断提高，在非常受欢迎的，高调的出版物中（Biiochemistry，2006 45（8）：2545-55）和会议上的互惠介绍。这种提高的知名度引起了UCSF以外的多个研究人员的兴趣，他们希望将SFLD用作自己的超家族信息的数据管理工具。未来工作的重点是开发工具和培训程序，以帮助这些研究人员利用SFLD来实现自己的研究目的。 SFLD可向公众提供http://sfld.rbvi.ucsf.edu。