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
RNF168-RING domain and nucleosome complex
Release Date: 2019-04-29
Publication doi: 10.1038/s41467-019-09756-z
Myeloid-derived growth factor with KDEL receptor
Release Date: 2019-12-18
Publication doi: 10.1038/s41467-019-13577-5
News
Updated Validation Reports
We are excited to share that we have updated PDB-Dev validation reports to version 1.1. The key feature of this update is the integration of the validation report generation workflow with the deposition and curation pipeline. Validation reports are now generated during the submission process, along with the issue of accession codes, making these reports available for depositors to review and share pre-release. Read more...
Casp16 Call for Targets
CASP (Critical Assessment of protein Structure Prediction) challenges are held every two years. The CASP organizers are now requesting targets for the upcoming 2024 CASP16 challenge. CASP targets can be directly submitted to CASP organizers or to the PDB. Read more...
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. Read more...