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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

基本信息

批准号：
1338415
负责人：
Stephen Burley
金额：
$ 3219.54万
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：
2014
资助国家：
美国
起止时间：
2014-04-01 至 2019-03-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1338415&HistoricalAwards=false
关键词：
PDB Management Research Collaboratory Structural

项目摘要

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 that is essential for 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 PDB will be managed by the Research Collaboratory for Structural Biology (RCSB), consisting of a partnership between Rutgers, the University of California San Diego and the Scripps Institute of Oceanography 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 infrastructure associated with the two main operational functions of the archive: data ingestion and processing, and data dissemination. Improvements include provision of a robust, high-throughput pipeline to manage ongoing increases in the volume and complexity of data submitted to PDB, development of query, analysis, visualization, and reporting tools to enhance access to PDB data, and develop a range of education and outreach activities that support the use of PDB data by teachers and students at all educational stages. 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 ?Structural View of Biology? and ?Molecule of the Month? will reach audiences nationally and globally. New activities to be introduced under the current award include increased outreach to under-represented communities and the development of annual theme topics to provide a focus for national integration of education activities involving structural biology. 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，对我们理解生命系统至关重要。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。 PDB将由结构生物学研究合作实验室（RCSB）管理，该合作实验室由罗格斯大学、加州圣地亚哥大学和斯克里普斯海洋学研究所组成，旨在提供一个单一的、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。除了继续运行主要的数据归档、接收和传播功能外，该项目还将对与档案的两个主要业务功能（数据接收和处理以及数据传播）有关的基础设施进行若干改进。改进包括提供一个强大的，高吞吐量的管道，以管理提交给PDB的数据量和复杂性的持续增长，开发查询，分析，可视化和报告工具，以提高对PDB数据的访问，并开发一系列教育和推广活动，支持教师和学生在所有教育阶段使用PDB数据。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？生物学的结构观？然后呢？本月分子？将覆盖全国和全球的观众。在目前的奖项下推出的新活动包括增加对代表性不足的社区的宣传，以及制定年度主题，为涉及结构生物学的教育活动的国家一体化提供重点。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。