Protein structure databanks

PDB Protein structure databank Collection of publicly available 3-D structures of proteins and nucleic acids http //www.rcsb.org/pdb... 

The size of the PDB is increasing very rapidly in the January 1994 full release of the databank there were 2327 coordinate entries of which 605 had appeared since the previous, October 1993, release. The entries comprise 2143 protein structures, together with 156 DNA, 18 RNA and 10 carbohydrate structures. The PDB also contains bibliographic references to more than 100 maeromolecular structures which have been published, but which have not been deposited in the PDB by the authors. Recently there has been strong pressure on journals to make deposition of coordinates in the PDB a condition of publication [31]. 

Brookhaven databank (protein structures) http Wwww.pdb.bnl.gov , ... 

Now, several software programs can be used to examine the secondary structure of proteins in the protein databank. In addition, computer simulation is being developed to visualize the secondary and tertiary structure of proteins, which occur within microseconds of the formation of the primary structure. These computer simulations are bound to provide a better insight into the protein structure and perhaps establish the rules of secondary and tertiary structure formations. 

Jones, D. T., and C. Hadley. 2000. Threading methods for protein structure prediction. In D. Higgins, and W. R. Taylor (eds.) Bioinformatics Sequence, Structure and Databanks. Heidelberg, Germany Springer-Verlag. 

PDB The Protein Data Bank, originally compiled at Brookhaven National Laboratory and currently distributed from http //www.rcsb.org, contains X-ray diffraction and NMR-based structural data of macromolecular structures such as proteins, nucleic acids, and entire viruses. The PDB is the primary structural databank for the 3-D coordinates of macromolecules and freely accessible on-line. 

Orengo C A, N P Brown and W R Taylor 1992 Fast Structure Alignment for Protein Databank flearchlng Proteins. Structure, Function and Genetics 14-139-167... 

Although this chapter is about the GenBank nucleotide database, GenBank is just one member of a community of databases that includes three important protein databases SWISS-PROT, the Protein Information Resomce (PIR), and the Protein DataBank (PDB). PDB, the database of nucleic acid and protein structures, is described in Chapter 5. SWISS-PROT and PIR can be considered secondary databases, curated databases that add value to what is already present in the primary databases. Both SWISS-PROT and PIR take the majority of their protein sequences from nucleotide databases. A small proportion of SWISS-PROT sequence data is submitted directly or enters through a journal-scanning effort, in which the sequence is (quite literally) taken directly from the published literature. This process, for both SWISS-PROT and PIR, has been described in detail elsewhere (Bairoch and Apweiller, 2000 Barker et al., 2000.)... 

Databanks for nucleic acid sequences are available see Walgate (1982) for Europe, and Lewin (1982) for the USA. A protein crystal-structure databank is maintained by the Brookhaven National Laboratory, Long Island, NY 11973, USA. 

It is estimated that transporters account for about 50% of drug targets. However, their modes of (selective) transport are only poorly understood. This is due to difficulties in membrane protein purification, expression, and crystallization (Caffrey, 2003), which is still in its childhood. As a consequence there exists a striking disproportion between the number of entries of resolved structures of soluble proteins and membrane proteins in the protein databank (PDB, http //www.pdb.org/). To date, only about 2% (1462 by Sept 2011) of the structures are from transmembrane proteins (75594 structures in total). Out of these there are only 302 unique structures (proteins of same type but from different spjecies are included) (Irvine). Moreover, a significant number of the membrane protein structures determined are at relatively low resolutions (Lindahl Sansom, 2008). 

This format was developed for the representation of three-dimensional protein structures in the databank of such structures built by the Brookhaven National Laboratory. It has, however, been widely adopted for showing protein structures. 

Different methods have been devised to represent proteins. A structure for porcine pancreatic procolipase is reported in the Protein Databank, as determined by NMR spectroscopy. Many such structures are reported without the hydrogen atoms, since their positions often cannot be determined experimentally. Most MM packages will add hydrogens. Figure 1.18 gives the hydrogen-free procolipase structure in line representation. 

Swiss-Prot ia a curated databank of information on protein sequence, structure and function. It can be found under http //www.ebi.ac.uk/swissprot/. 

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