Structural databases proteins

J Kuszewski, AM Gronenborn, CM Clore. Improving the quality of NMR and crystallographic protein stiaictures by means of a conformational database potential derived from structure databases. Protein Sci 5 1067-1080, 1996. 

David, G. (2005) Covell Linking tumor cell cytotoxicity to mechanism of drug action An integrated analysis of gene expression, small-molecule screening and structural databases. Proteins Structure, Function, and Bioinformatics, 59 (3), 403-433. 

A number of structured databases have been developed to classify proteins according to the three-dimensional structures. Many of these are accessible via the World Wide Web, T1 protein databanlc (PDB [Bernstein d al. 1977]) is the primary source of data about the stru tures of biological macromolecules and contains a large number of structures, but many i these are of identical proteins (complexed with different ligands or determined at differet resolutions) or are of close homologues. 

SCOP Structural Classification of Proteins. Hierarchical protein structure database... 

Holm L and C Sander 1994. The FSSP Database of Structurally Aligned Protein Fold Families. Ni Acids Research 22 3600-3609. 

Charifson P S, J J Corkery, M A Murcko and W P Walters 1999. Consensus Scoring A Method fc Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures int Proteins. Journal of Medicinal Chemistry 42 5100-5109. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

In the protein structure database PDB ( http //www. rcsb.org/pdb), by X-ray crystallography and NMR spectroscopy, experimentally solved 3D-protein structures are available to the public. Homology model building for a query sequence uses protein portions of known 3D-stmctures as structural templates for proteins with high sequence similarity. 

Two new computer-based resources were launched in the 1970s. One was the Cambridge Structural Database (CSD) [55], and the other was the Protein... 

Charifson PS, Corkery JJ, Murcko MA, Walters,WP. Consensus scoring a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem 1999 42 5100-9. 

Beurskens, P. T. In Crystallographic Computing 3 Data Collection, Structure Determination, Proteins and Databases Sheldrick, G. M., Kruger, C., Goddard, R., Eds. Oxford New York, 1985 p 216-226. 

There were a number of practical and theoretical issues to be addressed. A key scientific question was whether fixation in formalin modified antigens in a reversible or irreversible manner. To be more specific, was there any theoretical or prior scientific evidence that the effects of formalin fixation on proteins could be reversed, and if reversed, was the structure of protein restored to a sufficient degree for recovery of antigenicity With these key questions in mind, one of the authors (Shi) spent many days and nights in 1988 searching the chemical literature under somewhat adverse conditions, with a second job as an apprentice in a supermarket, and prior to the increased efficiency of such searches that is afforded today by the Internet and online databases. The answer was finally found in a series of studies of the chemical... 

Due to the ready accessibility of SH2 domains by molecular biology techniques, numerous experimentally determined 3D structures of SH2 domains derived by X-ray crystallography as well as heteronuclear multidimensional NMR spectroscopy are known today. The current version of the protein structure database, accessible to the scientific community by, e.g., the Internet (http //www.rcsb.org/pdb/) contains around 80 entries of SH2 domain structures and complexes thereof. Today, the SH2 domain structures of Hck [62], Src [63-66], Abl [67], Grb2 [68-71], Syp [72], PLCy [73], Fyn [74], SAP [75], Lck [76,77], the C- and N-terminal SH2 domain ofp85a [78-80], and of the tandem SH2 domains Syk [81,82], ZAP70 [83,84], and SHP-2 [85] are determined. All SH2 domains display a conserved 3D structure as can be expected from multiple sequence alignments (Fig. 4). The common structural fold consists of a central three-stranded antiparallel ft sheet that is occasionally extended by one to three additional short strands (Fig. 5). This central ft sheet forms the spine of the domain which is flanked on both sides by regular a helices [49, 50,60]. 

Merops (http //merops.sanger.ac.uk), database of peptidases and their proteinaceous inhibitors. Includes enzyme classification and nomenclature, external links to literature, and the structure of proteins of interest (if known). Enables one to find the gene coding for a given peptidase or to find the best enzyme to digest a chosen substrate. 

HSSP Homology-derived secondary structure of proteins database (HSSP)... 

Figure 2. Three-dimensional structure of human cytochrome c created by Protein Adviser, ver 3.0 (FQS, Hakata, Japan) with PDB file of human cytochrome c down-loaded from protein structure database of NCBI. a-Helices are shown as purple ribbons, random coils as white strands, and P-tums are blue (see separate colour tip). Heme c is depicted in white straight lines inside the protein.

---