ProtBuD：蛋白质家族和超家族的生物单元结构数据库。
ProtBuD: a database of biological unit structures of protein families and superfamilies.
作者信息
Xu Qifang, Canutescu Adrian, Obradovic Zoran, Dunbrack Roland L
机构信息
Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia, PA 19111 USA.
出版信息
Bioinformatics. 2006 Dec 1;22(23):2876-82. doi: 10.1093/bioinformatics/btl490. Epub 2006 Oct 2.
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.
动机
蛋白质相互作用的建模通常可以从相关复合物的已知结构中进行。找到最合适的模板往往很耗时。假设的生物学单元（BU）通常与不对称单元不同，通常最好从BU进行建模。
结果
ProtBuD是蛋白质数据库（PDB）中所有结构的BU数据库。我们同时使用PDB的BU和来自蛋白质四级结构服务器的BU。ProtBuD可通过PDB条目、蛋白质结构分类（SCOP）指定或SCOP指定对进行搜索。该数据库提供了PDB中相关蛋白质的不对称和BU内容，这些内容在SCOP和位置特异性迭代比对（PSI-BLAST）中得到了识别。对于52%的X射线结构，不对称单元与PDB和/或蛋白质四级结构服务器（PQS）的BU不同，并且PDB和PQS的BU在18%的条目中不一致。
可用性
该数据库以独立程序和网页服务器的形式提供，网址为http://dunbrack.fccc.edu/ProtBuD.php。
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