PDB Management by the Research Collaboratory for Structural Bioinformatics

结构生物信息学研究合作实验室的 PDB 管理

• 批准号: 0829586
• 负责人: Helen Berman
• 金额: $ 2841.4万
• 依托单位: Rutgers University New Brunswick
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-03-01 至 2014-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0829586&HistoricalAwards=false
• 关键词: PDB; Management; Research; Collaboratory; Structural

An award is made to Rutgers, the State University of New Jersey to manage the Protein Data Bank (PDB), an international repository and primary source for information about the structure of biological macromolecules. The PDB is a key research resource and a central component to our understanding of living systems. It serves a broad community of experimental, structural and computational scientists, and educators at all levels. PDB access is provided through primary web and ftp sites (www.pdb.org, ftp.pdb.org) or via multiple mirror sites distributed worldwide. The goal of the Research Collaboratory for Structural Biology (RCSB) in managing PDB is to provide a single, searchable archive of accurate and well-annotated data on experimentally determined macromolecular structure. Systems developed by RCSB are currently being used for data processing, archiving, distribution and query, as well as maintenance of the physical archive. In addition to continued operation of the primary data archiving, ingestion, and dissemination functions, the project will implement several enhancements to the existing infrastructure. First, they will introduce view interfaces to the PDB data aligned to specific user community interests such as model organisms, protein families, or ligand binding sites. Second, they will contribute to standards for quantitative representation of structural biology data via advanced data formats, metadata standards, software design, and data dissemination. Third, they will build upon the strengths of the international wwPDB partnership by introducing integrated data processing frameworks to improve efficiency and automation of data curation across the wwPDB partnership. Finally, the RCSB will continue to work with diverse communities to ensure the PDB resource best serves the interest if science, medicine, and education. The result of this effort will be a significant improvement in the utility and value of the Protein Data Bank for both specialists and non-specialists alike. Mechanisms for increasing the broader impacts of this work include the following: a series of workshops and meeting sessions, active participation in scientific meetings, a regular newsletter, the on-going use of a help desk to increase the access and utility of PDB for the specialist and non-specialist research community, and use of focus groups to insure maximum usability of PDB data. Participation in graduate and undergraduate coursework design and implementation and in structured research opportunities is being used to increase the impact of PDB on university-level education. Participation in teacher training workshops and a collaborative effort to launch a teacher development program provide opportunities to bring PDB resources to the K/12 environment. The general public is being made aware of PDB efforts through a traveling art exhibit and through frequent news releases and informational programs. Online-based activities like the Molecular Anatomy Project and Molecule of the Month will reach audiences nationally and globally. Collectively, these efforts will extend the benefits of PDB resources and activities to the broadest possible community.

授予罗格斯大学，新泽西的州立大学管理蛋白质数据库（PDB），一个国际知识库和生物大分子结构信息的主要来源。PDB是一个关键的研究资源，也是我们理解生命系统的核心组成部分。它为实验，结构和计算科学家以及各级教育工作者的广泛社区提供服务。 PDB访问是通过主Web和FTP站点（www.pdb.org、ftp.pdb.org）或通过分布在世界各地的多个镜像站点提供的。 结构生物学研究合作实验室（RCSB）管理PDB的目标是提供一个单一的、可搜索的、关于实验确定的大分子结构的准确且注释良好的数据档案。 目前正在使用区域公务员制度委员会开发的系统进行数据处理、归档、分发和查询，以及实物档案的维护。除了继续运行主要数据存档、接收和传播功能外，该项目还将对现有基础设施进行若干改进。首先，他们将为PDB数据引入视图界面，这些数据与特定用户社区的兴趣（如模型生物、蛋白质家族或配体结合位点）相一致。其次，他们将通过先进的数据格式、元数据标准、软件设计和数据传播，为结构生物学数据的定量表示标准做出贡献。第三，他们将通过引入集成数据处理框架，以提高整个wwPDB合作伙伴关系的数据管理效率和自动化程度，从而建立国际wwPDB合作伙伴关系的优势。最后，RCSB将继续与不同的社区合作，以确保PDB资源最好地服务于科学，医学和教育的利益。这一努力的结果将是蛋白质数据库对专家和非专家的效用和价值的显著提高。增加这项工作的广泛影响的机制包括：一系列讲习班和会议，积极参加科学会议，定期通讯，不断使用服务台，以增加专家和非专家研究界对PDB的访问和利用，以及使用焦点小组，以确保PDB数据的最大可用性。参与研究生和本科生课程的设计和实施以及结构化的研究机会正在被用来增加PDB对大学教育的影响。 参加教师培训研讨会和共同努力，推出教师发展计划提供了机会，使PDB资源的K/12环境。 通过巡回艺术展和频繁的新闻发布和信息节目，公众正在了解PDB的努力。 在线活动，如分子解剖学项目和本月分子将达到全国和全球观众。总的来说，这些努力将把PDB资源和活动的好处扩大到尽可能广泛的社区。