Welcome to PDB-Dev

PDB-Dev is a prototype archiving system for structural models obtained using integrative or hybrid modeling and is funded by the NSF ABI Development Program. Structural characterization of many complex macromolecular assemblies is increasingly carried out using integrative modeling, where a combination of complementary experimental and computational techniques is used to determine the structure. The structural models obtained through integrative modeling are collected, archived and disseminated to the public through PDB-Dev. Once the mechanisms for processing integrative models are fully established through PDB-Dev, the key components will be integrated with the wwPDB OneDep system and the PDB-Dev holdings will be moved into the PDB.


Released PDB-Dev Structures

News

New Deposition API

Starting January 22nd 2024, PDB-Dev accepts automated depositions of integrative structures via an API. Depositors can use a command line interface (CLI) tool to upload IHMCIF files and create new entries for submission. The tool has been implemented using the deriva-py python API provided by the DERIVA scientific asset management platform. The CLI tool is particularly useful for bulk uploads and for creating multiple entries belonging to a collection. Read more...


New feature - structure collections!

The PDB-Dev team is excited to announce a new feature - structure collections - to better reflect the links between structures generated within the scope of a single research project, investigation, or publication. With increasing numbers of structures generated through high-throughput experimental methods and artificial intelligence-based computational tools, such as AlphaFold and RoseTTAFold, structure collections allow for a convenient way of linking related entries. Read more...


First 100 structures in the PDB-Dev!

We are proud to announce an important milestone for PDB-Dev - the first 100 entries are released to the public. This achievement is a result of the continued collaboration among the PDB-Dev team, members of the wwPDB IHM task force, wwPDB leadership, RCSB PDB team members, and our pioneer depositors, who were the first to realize the importance of sharing the results of integrative structural biology investigations. Read more...


First AlphaFold-based structure in PDB-Dev

For a long time, the primary sources of starting structures for integrative modeling were experimental structures from the Protein Data Bank or computational models generated using various comparative modeling approaches. The recent machine learning revolution has led to the development of modeling methods like AlphaFold2 and RoseTTAFold, and also brought a whole new universe of high-quality predicted structures of proteins. Now these structures are finally making their way into integrative modeling. Read more...


Supported by
National Science Foundation