PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM)

YH
Yu He Liang
Wed, Aug 14, 2024 5:44 PM

Dear PDB-l

Structures determined by integrative and hybrid structure determination
methods (IHM) are now available alongside experimental structures in the
PDB archive. These structures are deposited into and processed by the
PDB-Dev system. Each IHM structure is issued a PDB ID, reported in the
PDBx/mmCIF file in the _database_2 category, and “integrative” method
provenance is captured at _struct.pdbx_structure_determination_methodology.
Users can access and download IHM structures and associated data at
files.wwpdb.org/pub/pdb_ihm/.

Currently, holding files in JSON format, validation reports (summary and
full reports) in PDF format, and model files in PDBx/mmCIF format are
provided.

Data may be expanded in the future based on community needs. In the near
future, IHM data will also be available via wwPDB DOI landing pages and
wwPDB partner websites.

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

--
YUHE LIANG, Ph.D.
Biocuration Lead Deputy, RCSB Protein Data Bank
Research Associate, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08554
P: 848.445.4938 | E: yuhe.liang@rcsb.org

Dear PDB-l Structures determined by integrative and hybrid structure determination methods (IHM) are now available alongside experimental structures in the PDB archive. These structures are deposited into and processed by the PDB-Dev system. Each IHM structure is issued a PDB ID, reported in the PDBx/mmCIF file in the _database_2 category, and “integrative” method provenance is captured at _struct.pdbx_structure_determination_methodology. Users can access and download IHM structures and associated data at files.wwpdb.org/pub/pdb_ihm/. Currently, holding files in JSON format, validation reports (summary and full reports) in PDF format, and model files in PDBx/mmCIF format are provided. - /pdb_ihm/holdings/ (current holdings, released structures last modified dates, unreleased entries) - /pdb_ihm/data/entries/hash/{PDB_id}/validation_reports/ (includes summary and full validation reports) - /pdb_ihm/data/entries/hash/{PDB_id}/structures/ (latest version of model files) - For example, https://files.wwpdb.org/pub/pdb_ihm/data/entries/zz/8zz1/structures/8zz1.cif.gz Data may be expanded in the future based on community needs. In the near future, IHM data will also be available via wwPDB DOI landing pages and wwPDB partner websites. Questions or feedback? Contact deposit-help@mail.wwpdb.org or pdb-dev@mail.wwpdb.org. -- YUHE LIANG, Ph.D. Biocuration Lead Deputy, RCSB Protein Data Bank Research Associate, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08554 P: 848.445.4938 | E: yuhe.liang@rcsb.org