Table 2.

Additions and updates to the PDBe REST API and FTP sites

PDBe REST API (pdbe.org/api)

• New endpoints for protein information.  ∘ CATHb structure domains.         ∘ Pre-release Pfam sequence domains (via HMMER).  ∘ Ensembl identifiers. • New endpoints for nucleic-acid information.  ∘ RNA molecules mapped to Rfam. • New endpoints for information on small molecules in the Chemical Component Dictionary (CCD).  ∘ Cofactor information.  ∘ Cross-references to DrugBank (including UniProtKB accessions for drug targets), ChEBI (22), ChEMBL (21) and CSD (37).

PDBe enriched FTP (ftp://ftp.ebi.ac.uk/pub/databases/msd)

• mmCIF-format assembly files added (ftp://ftp.ebi.ac.uk/pub/databases/msd/assemblies). ∘ These contain full assemblies for a given structure, along with rotation/translation operators required to generate the assemblies from the PDB entry file. ∘ Includes XML files summarizing the composition of the assembly files, relating each chain in the assembly to an entity in the PDB entry. • New FTP area for updated chemical-component process (ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2).  ∘ CCD mmCIF files with additional cross-references, mapped through the UniChem pipeline (38), to ChEMBL, DrugBank, KEGG, ChEBI, ZINC, Pubchem, NMRShiftDB, BindingDb, MetaboLights, BRENDA and Rhea.  ∘ Updated image files for molecules in CCD.  ∘ Coordinate data in various formats – including PDB and SDF.