BBSRC-NSF/BIO: From atoms to molecules to cells - Multi-scale tools and infrastructure for visualization of annotated 3D structure data

美国RCSB蛋白质数据库(RCSB PDB) -欧洲英国蛋白质数据库（PDBe）合作项目将重新设计现有的开源Molstar分子图形基础设施，以开发一个可扩展的一站式服务，用于可视化和查询开放获取的三维（3D）结构数据，这些数据集成自蛋白质数据库（PDB）、NextGen PDB、PDB- dev、电子显微镜数据库、电子显微镜图像存档和生物图像存档。Molstar完全适用于用户的互联网浏览器（例如，Chrome, Firefox, Safari）。它包含一个易于使用的图形界面，无需用户登录或软件产品下载、更新或注册。重新设计的Molstar系统将符合FAIR（可查找性、可访问性、互操作性和可重用性）和FACT（公平性、准确性、保密性、透明度）原则。它将支持有效的数据传输、可视化和3D结构数据的研究，以及从单个原子到整个细胞的长度尺度上的结构、生物和功能注释。访问新系统的研究人员、教育工作者和学生将能够从多个开放访问数据资源中组合、可视化和评估结构数据以及相关的生物、医学和化学信息。它还将支持生物分子在细胞器或细胞环境下的3D结构分析。重新设计的Molstar基础设施的用户将能够研究大分子机器（例如，原核RNA聚合酶-核糖体超级复合体；真核核核孔复合体），并结合来自美洲、欧洲、大洋洲和亚洲的各种开放获取生物数据资源的生物和功能信息，进行3D原位研究。该项目将解决存储在不同的开放访问主数据资源中的不断增长的3D结构数据所带来的重大挑战。这包括需要将这些数据与知识库中的相关生物和功能注释进行集成和互操作；需要一个标准的数据表示来显示跨长度尺度的3D结构数据；需要在一系列相关结构中检查生物大分子的多个3D结构，这些结构来自前沿技术，如连续飞秒x射线晶体学和低温电子显微镜；需要结合原子水平/多尺度结构与低温电子断层扫描和超分辨率显微镜的低分辨率信息；并且需要高效的数据打包、压缩和传输，以满足具有不同Internet连接级别的用户的需求。该项目将克服目前在数据管理、互操作性和可视化方面的限制，这些限制使得分子、细胞和生物生物学家很难，有时甚至不可能充分利用世界上开放的3D生物结构数据。该项目的软件产品将在https://www.molstar.org上免费提供。Molstar软件的使用将在RCSB PDB （https://www.rcsb.org）和PDBe （https://www.pdbe.org）的门户网站中举例说明。在最宽松的知识共享CC0 1.0通用许可（https://creativecommons.org/publicdomain/zero/1.0/）.This)下，所有用户都可以免费获得，并且对数据使用没有限制。该奖项反映了NSF的法定使命，并且通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This US RCSB Protein Data Bank (RCSB PDB) - UK Protein Data Bank in Europe (PDBe) collaborative project will significantly redesign existing open-source Molstar molecular graphics infrastructure to develop an extensible, one-stop-shop for visualization and interrogation of open-access three-dimensional (3D) structure data integrated from the Protein Data Bank (PDB), NextGen PDB, PDB-Dev, Electron Microscopy Data Bank, Electron Microscopy Image Archive, and BioImage Archive. Molstar works entirely with the users internet browser (e.g., Chrome, Firefox, Safari). It consists of an easy-to-use graphical interface with no user login or software product download, update, or registration required. The redesigned Molstar system will be FAIR (Findability, Accessibility, Interoperability, and Reusability) and FACT (Fairness, Accuracy, Confidentiality, Transparency) Principles compliant. It will support efficient data delivery and visualization and study of 3D structure data together with structural, biological, and functional annotations across length scales ranging from individual atoms to whole cells. Researchers, educators, and students accessing the new system will be able to combine, visualize, and evaluate structure data and related biological, medical, and chemical information from multiple open-access data resources. It will also support analyses of 3D structures of biomolecules their respective in organellar or cellular contexts Users of the redesigned Molstar infrastructure will be able to study macromolecular machines (e.g., prokaryotic RNA Polymerase-Ribosome Super Complex; eukaryotic Nuclear Pore Complex) in 3D in situ combined with biological and functional information integrated from a diverse array of open-access biodata resources operating in the Americas, Europe, Oceania, and Asia.This project will address significant challenges resulting from the growing corpus of 3D structure data stored in disparate open-access primary data resource. These include the need for integration and interoperation of these data with related biological and functional annotations from knowledgebases; the need for a standard data representation for display of 3D structure data across length scales; the need to examine multiple 3D structures of biological macromolecules in groups of related structures coming from cutting-edge techniques such as serial femtosecond X-ray crystallography and cryo-electron microscopy; the need to combine atomic level/multiscale structures with lower resolution information from cryo- electron tomography and super-resolution microscopy; and the need for efficient data packaging, compression, and delivery for users with diverse levels of internet connectivity. The project will overcome current limitations in data management, interoperability, and visualization that make it difficult, sometimes impossible, for molecular, cellular, and organismal biologists to fully utilize the world’s open-access 3D biostructure data. The software products of the project will be freely accessible at https://www.molstar.org. Utilization of the Molstar software will be exemplified within the web portals of RCSB PDB (https://www.rcsb.org) and PDBe (https://www.pdbe.org), which are available to all users at no charge and with no limitations on data usage under the most permissive Creative Commons CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0/).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.