Structure Database Primary Archive

Protein Data Bank (PDB) at http //www.rcsb.org/pdb/ is the worldwide archive of structural data of biomacromolecules (Kouranov et al, 2006). PDB was established at 

Aldehyde dehydrogenase AARSDB Aminoacyl-tRNA synthetases CAZy Carbohydrate active enzymes Esther Esterases and hydrolases G6P dehydrogenase HIV Proteases 

TABLE 16.5 Representative boutique databases for receptor and signaling proteins 

Endo GPCR List http //www.tumor-gene.org/GPCR/gpcr.html GPCR, expression 

HORDE http //bioinfo.weizmann.ac.il/HORDE/ Human olfactory R 

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One of the best known protein structure databases is the Protein Data Bank (PDB) [23]. PDB archives experimentally determined three-dimensional structures of biological macromolecules and contains atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data... 

Many biological databases (databanks) are embedded with tutorials that make it easy to explore their facilities. There are three sources of biological databases in-house dedicated sources (private and limited for focused projects), databases assembled by companies (mainly fees for services extensive and high-quality but expensive and restrictive such as Celera Genomics and Incyte Genomics), and public databases (such as GenBank, EMBL and DDBJ). An important distinction exists between primary (archival) and secondary (curated) databases. The primary databases represent experimental results with some interpretation (Table 14.11). Their record is the sequence or structure as it was experimentally derived. 

The Protein Data Bank (PDB) at Brookhaven National Laboratory is a database containing experimentally determined, three-dimensional structures of proteins, nucleic acids, and other biological macromolecules. The PDB has a history of service starting in 1971 to a global community of researchers, educators, and students in a variety of scientific disciplines. The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data. Scientists around the world contribute structures to the PDB and use it on a daily basis. The common interest shared by this community is a need to access information that can relate the biological functions of macromolecules to their three-dimensional structures. 

The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data. Annotations in the structure entries include amino acid or nucleotide sequences (with notes of any conflicts between the structure in the PDB and sequence databases), source organism from which the biological material was derived, references to papers, secondary structure, complexes with small molecules included within the structure, etc. Third party annotations include images and movies of structures, pointers to other databases which contain information on the structural class or family of the particular structure pointers to particular specialized databases (maintained by others) such as the kinase , esther , or obsolete entries databases, and those that provide additional experimental information such as NMR and other solution data, abstracts of articles, etc. 

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