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

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.