PDB-Dev now PDB-IHM

IP
Irina Persikova
Tue, Jan 21, 2025 2:48 PM

Structures of many large macromolecular assemblies are now being
determined using integrative approaches, wherein information derived
from multiple experimental and computational methods is combined to
compute their three-dimensional structures. PDB-IHM (formerly PDB-Dev)
is a system for archiving and disseminating structures determined using
integrative or hybrid methods (IHM), and making them Findable,
Accessible, Interoperable, and Reusable (FAIR).

In August 2024, PDB-Dev was unified with the PDB to deliver integrative
structures alongside experimental structures in the PDB archive
https://files.wwpdb.org/pub/. With unification, integrative structures
are assigned PDB accession codes and Digital Object Identifiers (DOIs),
annotated as IHM structures, and can be accessed from the PDB archive,
PDB DOI links (e.g., DOI: 10.2210/pdb8zzc/pdb
https://doi.org/10.2210/pdb8zzc/pdb), and the PDB-IHM website
https://pdb-ihm.org/. Now part of the PDB infrastructure, PDB-Dev has
been rebranded as PDB-IHM, denoting IHM structures archived in the PDB.

Integrative structures can be deposited through the PDB-IHM deposition
portal https://data.pdb-ihm.org/ and accessible from the wwPDB OneDep
home page https://deposit.wwpdb.org/. They are processed in parallel
to the wwPDB OneDep system https://deposit.wwpdb.org/. Structures
processed by PDB-IHM are released synchronously with PDB structures
weekly on Wednesdays at 00:00 UTC.

In the future, the wwPDB partners, including Research Collaboratory for
Structural Bioinformatics Protein Data Bank (RCSB PDB
https://rcsb.org/) in the United States, Protein Data Bank in Europe
(PDBe https://ebi.ac.uk/pdbe/), and Protein Data Bank Japan (PDBj
https://pdbj.org/), will disseminate integrative structures on their
respective websites.

We look forward to supporting the structural biology community with
depositing integrative structures to PDB-IHM https://pdb-ihm.org/.

Questions or feedback? Contact deposit-help@mail.wwpdb.org or
heldesk@pdb-ihm.org.

--
IRINA PERSIKOVA, Ph.D.
Deputy Biocuration Lead, RCSB Protein Data Bank
Research Associate, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4938 | E: irina.persikova@rcsb.org
mailto:irina.persikova@rcsb.org
rcsb.org <www.rcsb.org> | iqb.rutgers.edu http://iqb.rutgers.edu |
facebook https://www.facebook.com/RCSBPDB | twitter
https://twitter.com/buildmodels

Structures of many large macromolecular assemblies are now being determined using integrative approaches, wherein information derived from multiple experimental and computational methods is combined to compute their three-dimensional structures. PDB-IHM (formerly PDB-Dev) is a system for archiving and disseminating structures determined using integrative or hybrid methods (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). In August 2024, PDB-Dev was unified with the PDB to deliver integrative structures alongside experimental structures in the PDB archive <https://files.wwpdb.org/pub/>. With unification, integrative structures are assigned PDB accession codes and Digital Object Identifiers (DOIs), annotated as IHM structures, and can be accessed from the PDB archive, PDB DOI links (e.g., DOI: 10.2210/pdb8zzc/pdb <https://doi.org/10.2210/pdb8zzc/pdb>), and the PDB-IHM website <https://pdb-ihm.org/>. Now part of the PDB infrastructure, PDB-Dev has been rebranded as *PDB-IHM*, denoting IHM structures archived in the PDB. Integrative structures can be deposited through the PDB-IHM deposition portal <https://data.pdb-ihm.org/> and accessible from the wwPDB OneDep home page <https://deposit.wwpdb.org/>. They are processed in parallel to the wwPDB OneDep system <https://deposit.wwpdb.org/>. Structures processed by PDB-IHM are released synchronously with PDB structures weekly on Wednesdays at 00:00 UTC. In the future, the wwPDB partners, including Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB <https://rcsb.org/>) in the United States, Protein Data Bank in Europe (PDBe <https://ebi.ac.uk/pdbe/>), and Protein Data Bank Japan (PDBj <https://pdbj.org/>), will disseminate integrative structures on their respective websites. We look forward to supporting the structural biology community with depositing integrative structures to PDB-IHM <https://pdb-ihm.org/>. Questions or feedback? Contact deposit-help@mail.wwpdb.org or heldesk@pdb-ihm.org. -- IRINA PERSIKOVA, Ph.D. Deputy Biocuration Lead, RCSB Protein Data Bank Research Associate, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4938 | E: irina.persikova@rcsb.org <mailto:irina.persikova@rcsb.org> rcsb.org <www.rcsb.org> | iqb.rutgers.edu <http://iqb.rutgers.edu> | facebook <https://www.facebook.com/RCSBPDB> | twitter <https://twitter.com/buildmodels>