Unified Data Resource for 3DEM

描述(申请人提供)：三维透射电子显微镜(3DEM)正在成为一种强大的方法，用于确定大型生物组件在溶液中和细胞中的三维结构，从而能够阐明复杂的生物 相互作用对于理解细胞机械的内部工作方式是不可或缺的，并对基本的生物过程产生新的见解。现在，每年都有数百个3DEM实验在文献中报道，超过1300个结构可以通过EMDataBank(EMDataBank.org)在公共档案中找到。该项目的主要目标是建立评估这些结构的可靠性的方法，并为数据交换建立统一的标准，以便弥合目前3DEM与现有结构确定方法(X射线结晶学和核磁共振)在评估和解释实验结果方面的巨大差距。EMDataBank将在促进评估、建立和传播验证方法和数据标准所需的过程中发挥领导作用。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工作者提供的数据和软件包来建立。我们的结果将在EMDataBank网站上公开征求意见和审查。PDB交换词典将进行扩展，以支持3DEM社区评审的验证程序。通过该项目开发的MAP和MAP衍生模型验证程序将纳入蛋白质数据库的沉积和注释管道。这项工作预计将对3DEM和更广泛的生物科学界产生重大变革影响，使专家和非专家科学家能够对3DEM实验结果进行独立评估和解释，并提高3DEM结构数据的可靠性和一致性。

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.