[BiO BB] ProtBuD: A comparative database of biological units in the Protein Data Bank (PDB)

Struct Bio structbio at gmail.com
Mon Dec 4 19:20:12 EST 2006

We have developed ProtBuD, a database that contains information on the
contents of asymmetric units (ASUs) and hypothetical biological units
(BUs) as obtained from the PDB and the Protein Quaternary Server (PQS)
from the EBI (http://pqs.ebi.ac.uk).

A query consisting of a PDB entry code (e.g. 1TUP) retrieves ASU and
BU information across the family or superfamily as defined by SCOP and
PSI-BLAST relationships.  The database can also be queried by SCOP
family or superfamily code (e.g. b.2.5.2) or by a pair of such
designations to search for multi-domain proteins or complexes of
proteins. The database can also be used to search for specific content
a family or superfamily, such as complexes with ions, ligands, or nucleic

The biological unit from the PDB and/or PQS differ from the asymmetric
unit for 52% of X-ray structures.  The PQS and PDB BUs disagree with each
other for 18% of X-ray entries. For 14% of entries, the PDB BU is a
substructure of the PQS BU or vice versa. For 1.3% of entries, the PQS and
PDB entries differ and one is not a substructure of the other (i.e., they
different interfaces). For 3.3%, PQS lists an interface as a possible
crystallization artifact ("XPACK").

Availability: It is free to researchers in both non-profit and
commercial institutions. The database is provided as a standalone
program (recommended) and a web server from:


Reference: Qifang Xu, Adrian Canutescu, Roland Dunbrack,
Bioinformatics, vol. 22, pp. 2876-2882 (2006).

Roland Dunbrack
Fox Chase Cancer Center
Philadelphia PA 19111

Roland.Dunbrack at fccc.edu

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