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

冷冻电子显微镜确定的大型复合物的统一数据资源

• 批准号: 7318242
• 负责人: Wah Chiu
• 金额: $ 91.03万
• 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 2012-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7318242
• 关键词: Academia; Address; Adopted; Archives; Bioinformatics; Biological; Biological Models; Cells; Cellular biology; Collection; Communities; Complex; Computer software; Consensus; Consultations; Cryoelectron Microscopy; Crystallography; Data; Data Collection; Databases; Deposition; Development; Docking; Educational workshop; Electron Microscopy; European; Generations; Goals; Grant; Harvest; Health Services Accessibility; Image; Imagery; Industry; Institutes; Internet; Joints; Knowledge; Macromolecular Complexes; Maps; Medicine; Metadata; Methodology; Methods; Modeling; Molecular; New Jersey; Numbers; Online Systems; Production; Proteins; Provider; Purpose; Range; Research; Research Infrastructure; Research Institute; Research Personnel; Resolution; Resources; Retrieval; Roentgen Rays; Scientist; Services; Software Tools; Standards of Weights and Measures; Structural Models; Structure; System; Techniques; Time; Universities; Validation; base; collaboratory; college; data integration; data modeling; density; design; experience; frontier; improved; interoperability; macromolecular assembly; reconstruction; repository; research study; structural biology; technology development; three dimensional structure; tool

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.

描述（由申请人提供）：冷冻电子显微镜（cryoEM）是结构生物学中一种成熟的方法，能够在2至100 A的宽分辨率范围内测定大分子复合物和细胞的3D结构，其信息弥补了细胞生物学和晶体学/NMR之间的差距。现在，结构、分子和细胞生物学家普遍认为cryoEM图谱及其相关模型可以为后续假设驱动的研究和知识发现奠定基础。在过去的四年中，由英国Hinxton的欧洲生物信息学研究所（EBI）和美国新泽西州皮斯卡特维新泽西的罗格斯州立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已经达成了社区共识，即现在是时候建立公共支持的一站式cryoEM密度图沉积和检索设施了，原子模型和相关的元数据。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。这些研究人员在存档密度图（Kim Henrick），存档原子模型坐标（Kim Henrick，Helen Berman）以及cryoEM技术开发的所有方面都具有互补的专业知识，包括数据收集，地图生成，cryoEM地图约束建模，可视化，分割和注释（Wah Chiu）。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，为cryoEM地图，模型及其相关元数据创建一个全球沉积和检索网络，以及用于标准化地图格式转换，地图分割和评估，模型评估，可视化和数据集成的一些软件工具的Web服务。这些工具对于核查已存入的数据至关重要，也有助于有效利用存档数据。我们将与cryoEM软件的主要开发人员协商开发这些工具。在纳入Web服务之前，我们将使用当前数据资源中可用的地图和坐标数据评估这些工具是否适合预期用途。我们将充分记录这些工具的使用和限制。此外，随着该领域的发展和成熟，新的综合cryoEM数据资源将以简单的方式进行维护和扩展。最后，这项拟议研究的一个重要组成部分是在整个资助期间收集社区投入，以便最终系统将以最高标准设计和实施，以满足cryoEM专家和生物最终用户的需求。