Unified Data Resource for 3DEM

3DEM 统一数据资源

• 批准号: 9131440
• 负责人: Wah Chiu
• 金额: $ 29.66万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-15 至 2016-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9131440
• 关键词: Advisory Committees; Archives; Binding; Biological; Biological Process; Cells; Collaborations; Collection; Communities; Complex; Computer software; Data; Data Quality; Data Set; Databases; Deposition; Development; Dictionary; Electrons; Evaluation; Event; Feedback; Funding; Goals; Grant; Health; Human; Image; Imagery; Journals; Laboratories; Leadership; Literature; Maps; Metadata; Methodology; Methods; Modeling; Online Systems; Persons; Preparation; Procedures; Process; Proteins; Protocols documentation; Published Comment; Reader; Recommendation; Reporting; Research; Resolution; Resources; Retrieval; Role; Sampling; Scientist; Services; Solutions; Structure; System; Techniques; Testing; Transmission Electron Microscopy; Validation; Work; X-Ray Crystallography; base; data exchange; data format; data modeling; experience; file format; image processing; improved; innovation; insight; member; method development; novel; research study; three dimensional structure; tool; web site

DESCRIPTION (provided by applicant): Three-dimensional transmission electron microscopy (3DEM) is emerging as a powerful method for determining the three-dimensional structures of large biological assemblies in solution and in the cell, enabling elucidation of complex biological interactions that are integral to understanding the inner workings of cellular machinery, and yielding novel insights into fundamental biological processes. Hundreds of 3DEM experiments are now reported in the literature each year and more than 1,300 structures are available in public archives through EMDataBank (EMDataBank.org). The major goal of this project is to establish methods to assess the reliability of these structures and to create uniform standards for data exchange, in order to bridge the current substantial gap between 3DEM and established structure determination methods (X-ray crystallography and NMR) in the ability to evaluate and interpret the experimental results. EMDataBank will take a leadership role in facilitating the processes necessary to assess, establish, and disseminate validation methods and data standards. The approach will leverage the expertise and experience of the EMDataBank team in validation, standards, and 3DEM methods development. Validation methods for both 3DEM maps and map-derived models will be established using our own test data sets and software packages as well as those contributed by other electron microscopists. Our results will be made publicly available for comment and review on the EMDataBank website. The PDB exchange dictionary will be extended to support 3DEM community-reviewed validation procedures. Map and map-derived model validation procedures developed through this project will be integrated into the deposition and annotation pipeline of the Protein Data Bank. The work is expected to have a strong transformative impact on both the 3DEM and the wider bioscience communities, enabling independent assessment and interpretation of 3DEM experimental results by both expert and non-expert scientists, and leading to higher reliability and improved consistency of 3DEM structure data.

描述（由申请人提供）：三维透射电子显微镜（3DEM）正在成为一种用于确定溶液和细胞中大型生物组装体的三维结构的强大方法，从而能够阐明复杂的生物组装体。 这些相互作用对于理解细胞机制的内部运作是不可或缺的，并产生对基本生物过程的新见解。现在，每年有数百个3DEM实验在文献中报道，通过EMDataBank（EMDataBank.org），公共档案中有1,300多个结构。该项目的主要目标是建立方法来评估这些结构的可靠性，并建立统一的数据交换标准，以弥合目前3DEM和建立结构测定方法（X射线晶体学和NMR）之间的巨大差距，评估和解释实验结果的能力。EMDataBank将在促进评估、建立和传播验证方法和数据标准所需的进程方面发挥领导作用。该方法将利用EMDataBank团队在验证、标准和3DEM方法开发方面的专业知识和经验。3DEM地图和地图衍生模型的验证方法将建立使用我们自己的测试数据集和软件包，以及其他电子显微镜贡献。我们的研究结果将在EMDataBank网站上公开发表，供评论和审查。PDB交换字典将扩展到支持3DEM社区审查验证程序。通过该项目开发的地图和地图衍生模型验证程序将被集成到蛋白质数据库的沉积和注释管道中。这项工作预计将对3DEM和更广泛的生物科学界产生强大的变革性影响，使专家和非专家科学家能够独立评估和解释3DEM实验结果，并提高3DEM结构数据的可靠性和一致性。