ProtBuD

ProtBuD is a bioinformatics tool that assists in searching the Protein Data Bank database for biological units (BUs) for structures. The tool provides a comprehensive database of BUs for all structures in the PDB and the Protein Quaternary Server, which is searchable by PDB entry, Structural Classification of Proteins (SCOP) designation, or pairs of SCOP designations.

The tool is designed to address the time-consuming process of finding the most appropriate template for modeling protein interactions, as hypothesized biological units (BUs) often differ from the asymmetric units. Therefore, it is usually preferable to model from the BUs. ProtBuD solves this problem by providing a database of BUs, which can be used as the foundational structure for modeling protein interactions.

The database also provides the asymmetric and BU contents of related proteins in the PDB as identified in SCOP and Position-Specific Iterated BLAST (PSI-BLAST). The asymmetric unit is different from PDB and/or Protein Quaternary Server (PQS) BUs for 52% of X-ray structures, and the PDB and PQS BUs disagree on 18% of entries.