Unified Data Resource for 3DEM

3DEM 统一数据资源

• 批准号: 9902538
• 负责人: Wah Chiu
• 金额: $ 62.44万
• 依托单位: STANFORD UNIVERSITY
• 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 2022-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9902538
• 关键词: 3-Dimensional; Advisory Committees; Archives; Basic Science; Benchmarking; Binding; Biological; Cell physiology; Cells; Collaborations; Communication; Communities; Complex; Cryoelectron Microscopy; Data; Data Set; Databases; Deposition; Development; Electron Microscopy; Funding; Future; Generations; Infrastructure; Investigation; Literature; Mainstreaming; Maps; Measures; Methodology; Methods; Modeling; Molecular Structure; Nucleic Acids; Outcome; Persons; Polymers; Positioning Attribute; Protocols documentation; Recommendation; Reporting; Resolution; Sampling; Services; Side; Statistical Data Interpretation; Statistical Methods; Statistical Models; Structure; System; Techniques; Translational Research; Transmission Electron Microscopy; Uncertainty; Validation; Vertebral column; annotation system; base; complex data; computerized data processing; data resource; density; experience; experimental study; image processing; improved; innovation; macromolecular assembly; meetings; model building; novel; nucleic acid structure; stereochemistry; structural biology; three dimensional structure; tool; web site

Abstract Three-dimensional transmission electron microscopy (3DEM) has become a cutting-edge method for determining structures of large biological assemblies due to recent technical advances. Hundreds of 3DEM experiments are reported in the literature each year and more than 4400 structures are now available in public archives through our EMDataBank.org website. Since 2014, following the cryo-electron microscopy "resolution revolution," more than 500 maps with resolutions better than 5.0 Å have been released, most with associated coordinate models. It is critically important that 3DEM maps and the models derived from them are of the highest possible quality, and to achieve this aim it is necessary to have community-accepted validation measures. In our current funding period we developed and promoted new methods and infrastructure to determine map accuracy and resolution, as well as novel methods to build and validate map-derived models. In addition, we hosted challenges and meetings to involve the 3DEM and modeling communities in developing new map and model validation standards. We also significantly expanded the underlying representation for 3DEM experimental methods, and collaborated to fully integrate 3DEM into the wwPDB Deposition and Annotation system. We propose here to continue to develop innovative solutions for validating 3DEM-derived structures of macromolecular assemblies, focusing on the moderate to high resolution range, 5-2 Å. To achieve this we will host new challenges formulated to engage the community using increasingly complex data derived by 3DEM methods and provide statistical analysis of their outcomes. In addition, we will develop and evaluate computational protocols that yield quantifiable parameters for validating 3DEM-derived structures, in terms of density map resolvability, map and model correlation and atom position uncertainty of the associated model. We will also improve the validation criteria for nucleic acids, which occur in 30% of all 3DEM derived models. We will use the EMDataBank website to disseminate the results of our investigations and to provide a platform for community engagement and discussions. Our approach will continue to build on the decades of experience of our team in developing tools for 3DEM map generation and modeling, analyzing large assemblies especially those containing nucleic acids, and working with the community to create standards for structure validation.

摘要 三维透射电子显微镜（3DEM）已成为一种尖端的方法， 由于最近的技术进步，确定大型生物组件的结构。数百个3DEM 每年都有文献报道这些实验，现在已有4400多个结构公开发表 通过我们的EMDataBank.org网站存档。自2014年以来，继冷冻电子显微镜“分辨率 革命，”超过500个地图与分辨率优于5.0毫米已经发布，大多数与相关 坐标模型至关重要的是，3DEM地图和从中导出的模型是 尽可能高的质量，为了实现这一目标，有必要进行社区接受的验证 措施在我们目前的资助期间，我们开发和推广了新的方法和基础设施， 确定地图精度和分辨率，以及建立和验证地图衍生模型的新方法。 此外，我们还举办了挑战赛和会议，让3DEM和建模社区参与开发 新的地图和模型验证标准。我们还显著扩展了 3DEM实验方法，并合作将3DEM完全集成到wwPDB沉积和 注释系统。我们建议继续开发创新的解决方案，以验证3DEM衍生的 大分子组装体的结构，集中在中等到高分辨率范围，5-2 μ m。到 为了实现这一目标，我们将举办新的挑战，利用日益复杂的数据吸引社区参与 通过3DEM方法得出，并提供其结果的统计分析。此外，我们将开发和 评估产生可量化参数的计算协议，用于验证3DEM衍生结构， 密度图的可分辨性，地图和模型的相关性和原子位置的不确定性， 模型我们还将改进核酸的验证标准，在所有3DEM中， 模型我们将利用EMDataBank网站发布我们的调查结果，并提供 社区参与和讨论的平台。我们的做法将继续建立在几十年来， 我们的团队在开发3DEM地图生成和建模工具，分析大型 特别是那些含有核酸的组件，并与社区合作， 结构验证