Recent updates to PDB-Dev, including the development of a new data harvesting system, have been published in Acta Crystallographica Section D: Vallat B et al., New sytem for archiving integrative structures, Acta Cryst. 2021; D77: 1486-1496. doi:10.1107/S2059798321010871
We have developed a new Data Harvesting System that provides a web interface for depositors to assemble all the information required for archiving integrative structures in PDB-Dev and to create a compliant mmCIF file. This includes the submission of integrative structures, associated spatial restraints and starting models used, modeling protocols and metadata information (citations, authors, software, data in external repositories, reference sequence information etc.).
The data harvesting system provides an automated mechanism for collecting diverse and heterogeneous types of integrative structures and restraint data. The system has been developed using the DERIVA scientific asset management platform and is based on the definitions in the IHM-dictionary and the parent PDBx/mmCIF dictionary.
A User Guide has been created with documentation regarding creating accounts and submitting data.
Recently, the PDB-Dev team participated in the BioExcel webinar series. The webinar presentation was titled "PDB-Dev: A prototype system for archiving integrative structures". The recorded version of the webinar is available on youtube.
3D visualization of structures using Molstar is now available on PDB-Dev. Structures in PDB-Dev can be directly visualized from the respective entry pages. Molstar can visualize atomic as well as multi-scale structures.
Integrative structures can also be visualized online using the Molstar viewer.
Molstar is an open collaboration started by PDBe and RCSB PDB to provide a technology stack for data delivery and analysis tools of macromolecules.
The PDB-Dev web interface has been revamped to provide dynamic, responsive and mobile-friendly web pages. The newly designed website has been made possible due to an overhaul of our backend infrastructure.
The PDB-Dev website now includes a new service that facilitates search and retrieval of integrative structures archived in PDB-Dev. Simple search using macromolecular names (e.g., nuclear pore complex), entry identifiers (e.g., PDBDEV_00000012), experimental methods used (e.g., NMR, 3DEM, CX-MS), author names (e.g., Sali), software used (e.g., IMP, HADDOCK, ROSETTA), and several other keywords are now supported. Search results can be downloaded as CSV or EXCEL files.
We have also added individual entry pages that provide a summary of the structure (title, description, authors) along with other details regarding the citation, software, input data, and links to related resources and downloading the structure.
In March 2019, a satellite workshop titled “Working towards federating structural models and data” was held at the Biophysical Society Annual meeting in Baltimore, Maryland to assess current progress and discuss further requirements for archiving integrative structures. The primary goal of the workshop was to bring together experts from different scientific communities contributing to integrative structural biology and build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validation of integrative structures. A whitepaper summarizing the outcomes of the workshop was recently published in the journal Structure.
The integrative structures can be downloaded as text files (use right click + save as) and opened on ChimeraX using the "format ihm" command line option along with the complete path to the downloaded file:
open path/to/myfile.cif format ihm
Alternately, the following command can be used to directly visualize an entry from PDB-Dev, eg: PDBDEV_00000010.
open 10 from pdbdev ignoreCache true
The PDB-Dev entry files have been recently updated to comply with updates in the IHM dictionary.
Older files downloaded from PDB-Dev will not be supported on the latest ChimeraX. Similarly, the new PDB-Dev files will not be supported on older versions of ChimeraX.
Please download a fresh copy of the file from PDB-Dev and/or clear the ChimeraX cached IHM files (delete ~/Downloads/ChimeraX/PDBDev) for visualizing the updated files with the latest ChimeraX.