ProtBuD


17018535	ProtBuD: a database of biological unit structures of protein families and superfamilies. [PMID: 17018535] Xu Q, Canutescu A, Obradovic Z, Dunbrack RL. Abstract MOTIVATION: Modeling of protein interactions is often possible from known structures of related complexes. It is often time-consuming to find the most appropriate template. Hypothesized biological units (BUs) often differ from the asymmetric units and it is usually preferable to model from the BUs. RESULTS: ProtBuD is a database of BUs for all structures in the Protein Data Bank (PDB). We use both the PDBs BUs and those from the Protein Quaternary Server. ProtBuD is searchable by PDB entry, the Structural Classification of Proteins (SCOP) designation or pairs of SCOP designations. The database 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. AVAILABILITY: The database is provided as a standalone program and a web server from http://dunbrack.fccc.edu/ProtBuD.php. Bioinformatics. 2006:22(23) \| 29 Citations (from Europe PMC, 2025-03-29)

ProtBuD: a database of biological unit structures of protein families and superfamilies. [PMID: 17018535]

Xu Q, Canutescu A, Obradovic Z, Dunbrack RL.

MOTIVATION: Modeling of protein interactions is often possible from known structures of related complexes. It is often time-consuming to find the most appropriate template. Hypothesized biological units (BUs) often differ from the asymmetric units and it is usually preferable to model from the BUs.
RESULTS: ProtBuD is a database of BUs for all structures in the Protein Data Bank (PDB). We use both the PDBs BUs and those from the Protein Quaternary Server. ProtBuD is searchable by PDB entry, the Structural Classification of Proteins (SCOP) designation or pairs of SCOP designations. The database 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.
AVAILABILITY: The database is provided as a standalone program and a web server from http://dunbrack.fccc.edu/ProtBuD.php.

Bioinformatics. 2006:22(23) | 29 Citations (from Europe PMC, 2025-03-29)

URL:	http://dunbrack.fccc.edu/ProtBuD
Full name:	a database of biological unit structures of protein families and superfamilies
Description:	ProtBuD is a database of hypothesized biological units for all structures in the Protein Data Bank (PDB). The database provides the asymmetric and BU contents of related proteins in the PDB as identified in SCOP and Position-Specific Iterated BLAST (PSI–BLAST).
Year founded:	2006
Last update:
Version:
Accessibility:	Accessible
Country/Region:	United States

Data type:	Protein
Data object:	Animal Archaea Bacteria Fungi Plant Virus
Database category:	Interaction Metadata
Major species:	Homo sapiens
Keywords:	biological units oligomers of a template interactions with nucleic acids interactions with other ligand

University/Institution:	Institute for Cancer Research
Address:	Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia, PA 19111 USA.
City:	Philadelphia
Province/State:
Country/Region:	United States
Contact name (PI/Team):	Roland L. Dunbrack
Contact email (PI/Helpdesk):	Roland.Dunbrack@fccc.edu

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Database Commons a catalog of worldwide biological databases