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

合作研究：创建机制，使蛋白质数据库中的大分子组装体的整合结构可用

• 批准号: 2112966
• 负责人: Brinda Vallat
• 金额: $ 72万
• 依托单位: Rutgers University New Brunswick
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2112966&HistoricalAwards=false
• 关键词: Collaborative; Research; Creating; mechanisms; make

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.

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从蛋白质数据库（PDB）中可用。PDB是生物大分子及其复合物三维结构的单一全球资源库。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提供对整合结构的开放访问，这将大大提高对细胞和分子生物学的理解，并加速生物医学和生物技术研究的进展。该项目是创建一个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。这项工作将通过PDB使每个人都能容易地获得复杂大分子组装的结构，从而大大推进生物学研究。越来越多地，许多复杂的生物组件的结构是使用综合方法确定的，其中来自多种实验方法的数据被结合在一起。使用单一方法确定的PDB档案结构需要扩展以处理这些集成结构。在过去的三年中，开发了一个名为PDB-Dev的独立原型系统，用于存档集成结构并使其公开可用。当前的项目将集成PDB- dev系统和PDB数据处理管道，并确保根据FAIR（可查找、可访问、可互操作和可重用）原则从PDB提供集成结构。PDB- dev与PDB的集成将使广泛且不断增长的PDB用户社区能够访问更丰富、更多样化的精心设计的结构模型集。该项目将通过PDB创建一个严格的标准化过程，用于沉积、策展、验证、存档和传播综合结构。这种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。该项目的结果可在PDB-Dev网站上访问：https://pdb-dev.wwpdb.org.This该奖项反映了美国国家科学基金会的法定使命，并通过基金会的智力价值和更广泛的影响审查标准进行评估，认为值得支持。

项目成果

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models

• DOI: 10.1016/j.jmb.2023.168021
• 发表时间: 2023-06-24
• 期刊: JOURNAL OF MOLECULAR BIOLOGY
• 影响因子: 5.6
• 作者: Vallat, Brinda;Tauriello, Gerardo;Westbrook, John D.
• 通讯作者: Westbrook, John D.