Unified Data Resource for Large Complexes Determined by Cryo-Electron Microscopy

描述(申请人提供)：低温电子显微镜(CREYO-EM)是结构生物学领域一种成熟的方法，它能够在2到100安的宽分辨率范围内确定大分子复合体和细胞的3D结构，并提供弥合细胞生物学和结晶学/核磁共振之间的信息。现在结构生物学家、分子生物学家和细胞生物学家都很好地接受了这一点，即低温EM图及其相关模型可以形成后续假设驱动的研究和知识发现的基础。在过去的四年里，由英国欣克斯顿的欧洲生物信息学研究所(EBI)和美国罗格斯大学的结构生物信息学研究合作实验室(RCSB)组织的几个独立研讨会达成了社区共识，即现在是时候为低温电磁密度图、原子模型和相关元数据建立公共支持的一站式存储和检索设施了。这项提议是EBI、RCSB和休斯顿贝勒医学院国家大分子成像中心(NCMI)的研究人员共同努力的结果。这些研究人员在归档密度图(Kim Henrick)、原子模型坐标归档(Kim Henrick、Helen Berman)以及CryoEM技术开发的方方面面，包括数据收集、地图生成、CryoEM地图受限建模、可视化、分割和注释(Wah Chiu)方面拥有互补的专业知识。我们建议整合三个成熟的研究中心的专业知识和基础设施，以创建一个全球沉积和检索网络，用于CryoEM地图、模型及其关联元数据，并为一些软件工具提供网络服务，用于标准化地图格式转换、地图分割和评估、模型评估、可视化和数据集成。这些工具对于核查已交存数据至关重要，也将有助于有效利用已存档数据。我们将与CryoEM软件的主要开发商协商开发这些工具。在纳入Web服务集合之前，我们将使用当前数据资源中提供的地图和坐标数据，评估这些工具是否适合预期目的。我们将详细记录这些工具的用法和限制。此外，随着领域的发展和成熟，新的、全面的CryoEM数据资源将以一种易于维护和扩展的方式建立。最后，这项拟议研究的一项重要组成部分活动是在整个赠款期间收集社区意见，以便最终系统将以最高标准设计和实施，以满足低温机械专家和生物最终用户的需求。

DESCRIPTION (provided by applicant): Cryo-electron microscopy (cryoEM) is a maturing methodology in structural biology that enables the determination of 3D structures of macromolecular complexes and cells at a broad range of resolution from 2 to 100 A with information that bridges the gap between cell biology and crystallography/NMR. It is now well accepted by structural, molecular and cell biologists that a cryoEM map and its associated model can form the basis for subsequent hypothesis-driven research and knowledge discovery. In the past four years, several independent workshops organized by the European Bioinformatics Institute (EBI) in Hinxton, UK and the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers, the State University of New Jersey, Piscataway, NJ, USA, have reached a community consensus that it is time to establish publicly supported, one-stop deposition and retrieval facilities for cryoEM density maps, atomic models and associated metadata. This proposal is a joint effort among investigators of the EBI, RCSB and the National Center for Macromolecular Imaging (NCMI) at Baylor College of Medicine, Houston. These investigators have complementary expertise in archiving density maps (Kim Henrick), archiving coordinates of atomic models (Kim Henrick, Helen Berman), and all aspects of cryoEM technology development, including data collection, map generation, cryoEM map restrained modeling, visualization, segmentation and annotation (Wah Chiu). We propose to integrate the expertise and infrastructure of the three well-established research centers to create a global deposition and retrieval network for cryoEM maps, models and their associated metadata, as well as a web service for a number of software tools for standardized map format conversion, map segmentation and assessment, model assessment, visualization, and data integration. These tools are essential for verification of the deposited data and would also facilitate efficient use of the archived data. We will develop these tools in consultation with the major developers of cryoEM software. Before inclusion in the set of web services, we will evaluate the suitability of these tools for the intended purposes with the map and coordinate data available in the current data resources. We will fully document the usage and limitations of these tools. Moreover, the new, comprehensive cryoEM data resource will be built in a manner that will be straightforward to maintain and extend as the field grows and matures. Finally, an important component activity of this proposed research is to gather community input throughout the entire grant period so that the final system will be designed and implemented at the highest standards to serve the needs of both cryoEM experts and biological end-users.