ASTRAL: Foundation for structure and evolution studies

ASTRAL：结构和进化研究的基础

• 批准号: 7478632
• 负责人: John-Marc Chandonia
• 金额: $ 21.62万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-09-23 至 2010-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7478632
• 关键词: Algorithms; Automation; Bioinformatics; Biomedical Research; Classification; Collection; Communities; Computer software; Data; Data Analyses; Databases; Development; Ensure; Evolution; Face; Familiarity; Feedback; Foundations; Libraries; Licensing; Maintenance; Measures; Methods; Molecular; Process; Production; Protein Databases; Proteins; Publications; Purpose; Research; Research Personnel; Resources; Running; Score; Staging; Standards of Weights and Measures; Structural Biologist; Structure; System; Time; base; cost; experience; improved; innovation; open source; programs; protein structure; statistics; tool

DESCRIPTION (provided by applicant): The ASTRAL compendium is a collection of software and databases used to aid research into protein structure and evolution. It is complementary to the SCOP: Structural Classification of Proteins database, created by our colleagues at the MRC in Cambridge, UK. SCOP is a comprehensive ordering of domains from all proteins of known structure according to their structural and evolutionary relationships. ASTRAL serves three major purposes: to provide the authoritative sequences and coordinate sets for domains in SCOP, to detect and eliminate errors in the SCOP classification, and to provide additional software and databases to aid in the analysis of the data in SCOP. These additional data include quantitative scores that assign a measure of quality to each crystallographically determined PDB entry in SCOP, representative subsets of PDB chains and SCOP domains, and ASTEROIDS, a system for preliminary classification of domains from newly solved PDB entries within the SCOP framework. ASTRAL development to date has been driven by the needs of our users, who are primarily structural biologists who require SCOP data in easily accessible formats, but lack the resources or expertise to accurately generate the data themselves. Another major group of users are bioinformaticists who use the ASTRAL subsets as a standard representative cross-section of protein structures on which to develop or compare algorithms. A third important group of users are developers of other databases, such as SUPERFAMILY and PRODOM, which are derived from the data in ASTRAL. Our specific aims in this project are to: 1. Produce, develop, and maintain ASTRAL to ensure its long-term utility, in particular: a) Further automate the software used to build ASTRAL. b) Fully document all tools used to build ASTRAL, and make them available as open source. c) Continue to produce new releases of ASTRAL. 2. Extend ASTRAL'S utility to more of the biomedical research community. 3. Develop resources to facilitate extension of ASTRAL by the bioinformatics community.

描述（由申请人提供）：ASTRAL纲要是用于帮助研究蛋白质结构和进化的软件和数据库的集合。它是补充SCOP：蛋白质结构分类数据库，由我们的同事在英国剑桥的MRC创建。SCOP是根据已知结构的所有蛋白质的结构和进化关系对结构域进行的全面排序。ASTRAL服务于三个主要目的：为SCOP中的域提供权威序列和坐标集，检测和消除SCOP分类中的错误，并提供额外的软件和数据库，以帮助分析SCOP中的数据。这些额外的数据包括定量评分，其为SCOP中每个晶体学确定的PDB条目分配质量度量，PDB链和SCOP结构域的代表性子集，以及ASTEROIDS，一种用于对SCOP框架内新解决的PDB条目进行初步分类的系统。 迄今为止，ASTRAL的发展一直是由我们的用户的需求驱动的，这些用户主要是结构生物学家，他们需要易于访问的格式的SCOP数据，但缺乏资源或专业知识来准确地生成数据。另一个主要的用户群是生物信息学家，他们使用ASTRAL子集作为蛋白质结构的标准代表性横截面，以开发或比较算法。第三个重要的用户群体是其他数据库的开发人员，如SUPERFAMILY和PRODOM，这些数据库是从ASTRAL的数据派生出来的。 我们在这个项目中的具体目标是： 1.生产、开发和维护ASTRAL，以确保其长期效用，特别是： （a）进一步使用于建造ASTRAL的软件自动化。 B）完整记录用于构建ASTRAL的所有工具，并将其作为开放源代码提供。 c）继续制作ASTRAL的新版本。 2.将ASTRAL的实用程序扩展到更多的生物医学研究社区。 3.开发资源，促进生物信息学界推广ASTRAL。