New Features

Search by Chemical Formula or Descriptor

09/25

Use the Advanced Search>Chemical Search option to find chemical components (standard and modified amino acids/nucleotides, and ligands) by Formula (exact match or portion) or SMILES or InChi descriptor (graph-relaxed, graph-relaxed-stereo, graph-strict, fingerprint-similarity). A description of this functionality is available.

Advanced Search Query Builder can be used combine these Chemical Searches with other types of searches using Boolean operators (AND/OR/NOT):

  • Attribute searching: specific fields or full-text search across all fields, such as ID, deposition information, entry features, and experimental information
  • Sequence searching: based on a FASTA sequence (with E-value or % Identity cutoffs);
  • Sequence Motif searching: find short sequence patterns in PDB structure FASTA sequences using Simple, PROSITE, or RegEx syntax
  • Structure Similarity searching: based on an existing Chain or Assembly of a PDB structure

The Attribute search can be used to find Chemical Components based on Name, Synonyms, Chemical Component Type, InChiKey, Molecular Weight, Atom Count, eternal database IDs, and binding affinity.

Advanced Search results can be returned as PDB structures, polymer entities, assemblies, or non-polymer entities that correspond to the search performed.

Small molecules in the PDB are described in the wwPDB Chemical Component Dictionary.

Information about small molecules in the PDB can be found in individual Ligand Summary pages (e.g., <a href="https://www.rcsb.org/ligand/B12">B12</a>)Information about small molecules in the PDB can be found in individual Ligand Summary pages (e.g., B12)