Collaborative Research: Creating mechanisms to make integrative structures of large macromolecular assemblies available from the Protein Data Bank

该项目的目标是开发必要的基础设施，使生物分子系统的综合结构可以从蛋白质数据库(PDB)获得。PDB是生物大分子及其络合物的三维结构的单一全球储存库。全世界数以百万计的科学家和教育工作者都在使用它。该项目将通过PDB提供对一体化结构的开放访问，这将极大地增强对细胞和分子生物学的了解，并加快生物医学和生物技术研究的进展。该项目是建立结构生物学资源互操作网络的核心，该网络将提供对研究数据的无缝访问，并促进有效的数据共享。这项工作将极大地推动生物学研究，使每个人都可以通过PDB轻松地获得复杂的大分子组件的结构。此外，许多复杂的生物组件的结构是使用综合方法确定的，其中结合了多种实验方法的数据。PDB对使用单一方法确定的结构进行存档，并且需要扩展以处理这些综合结构。在过去的三年里，已经开发了一个独立的原型系统，称为PDB-Dev，用于对综合结构进行归档并将其公开使用。目前的项目将把PDB-Dev系统与PDB数据处理管道相结合，并确保根据公平(可查找、可访问、可互操作和可重复使用)原则从PDB获得综合结构。PDB-Dev与PDB的集成将使广泛且不断增长的PDB用户社区能够获得更丰富、更多样化的精心策划的结构模型。该项目将建立一个严格的标准化程序，通过公共规划委员会对综合结构进行存放、管理、验证、存档和传播。这一功能将有助于解决越来越具有挑战性的结构确定问题，例如阐明完整基因组的三维结构，甚至创建整个细胞的时空模型。该项目的结果可从pdb-dev网站获取：https://pdb-dev.wwpdb.org.This奖反映了国家科学基金会的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

The goal of this project is to develop the necessary infrastructure to make the integrative structures of biomolecular systems available from the Protein Data Bank (PDB). PDB is the single global repository for three-dimensional structures of biological macromolecules and their complexes. It is used by millions of scientists and educators worldwide. This project will provide open access to integrative structures through the PDB, which will greatly enhance the understanding of cellular and molecular biology and speed the progress of biomedical and biotechnology research. The project is central to the creation of an interoperating network of structural biology resources that will provide seamless access to research data and promote efficient data sharing. This work will significantly advance biological research by making structures of complex macromolecular assemblies easily accessible to everyone through the PDB.Increasingly, structures of many complex biological assemblies are determined using integrative approaches, in which data from multiple experimental methods are combined. The PDB archives structures determined using single methods and needs to be expanded to handle these integrative structures. In the last three years, a standalone prototype system, called PDB-Dev, has been developed for archiving integrative structures and making them publicly available. The current project will integrate the PDB-Dev system with the PDB data processing pipeline and ensure that the integrative structures are made available from the PDB according to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. Integration of PDB-Dev with the PDB will enable the broad and growing community of PDB users to have access to an even richer and more diverse set of curated structural models. The project will create a rigorous standardized process for deposition, curation, validation, archival, and dissemination of integrative structures through the PDB. This functionality will facilitate tackling increasingly more challenging structure determination problems such as elucidation of the three-dimensional structures of complete genomes and even the creation of a spatiotemporal model of an entire cell. The results of the project can be accessed from the PDB-Dev website: https://pdb-dev.wwpdb.org.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.