Databases Brookhaven

PDB Databases Brookhaven Protein Data Bank Brookhaven National Laboratory... 

Figure 4.102 Crystal structure of ribonuclease A with the deamidation site at Asn. (Source Protein Database, Brookhaven National Labs, original data from Esposito et al. [94]).

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

HyperChem contains a database of amino and nucleic acid residues so you can quickly build polymers con laining these subunits. You can also read in structures in files from standard databases, such as the Brookhaven Protein Data Bank (see the HyperChem Reference Manual). 

Nuclear Data Sheets, Academic Press, San Diego, Calif., TvaluatedNuclear Structure Data File (ENSDF), a computer database of nuclear stmcture data evaluated by an international network of evaluators, is maintained at the National Nuclear Data Center, Brookhaven National Laboratory. NUDNTis a computer database of decay data extracted from the ENSDF. 

Another major source are the amino acid sequences direcdy derived from protein sequencing. Thousands of such sequences have been detected by the SWISS-PROT curators in publications (or have been directly submitted by researchers to SWISS-PROT) and entered into the database. Protein sequences detected by the NCBI journal scan have also been included. For some proteins the Brookhaven Protein Data Bank (PDB) (Abola et al., 1996) is the only source for the sequence information. The PDB entries are checked regularly, and new SWISS-PROT entries were created whenever necessary. 

In mid-1997 an international conference took place in Santa Cruz, USA, in which, for the first time, the exclusive topic was structural aspects of RNA molecules. A report covering this meeting contains an impressive graphic which shows the RNA structures, RNA/DNA complexes, and RNA/protein complexes contained in the brookhaven database as a function of the year of their publication [29]. Between 1988 and 1993 there were just 20. However, in 1996 alone no less than 41 structures appeared. These new dimensions were headed by the crystal structural elucidation of the first larger RNA molecule since the first crystal structure of tRNA in 1973 [30], the 48 nucleotide long hammerhead ribo-zyme (HHR) [31-33]. This landmark achievement was followed by a crystal structure analysis of the P4-P6-domain of a group I intron [34-36] and, more recently, a crystal structure of the hepatitis delta virus ribozyme [37]. 

Molecular structure data bases are particularly useful in the analysis and engineering of zinc coordination polyhedra, and statistical results from the Brookhaven Protein Data Bank (Bernstein et al., 1977) and the Cambridge Structural Database (Allen et al., 1983) are presented... 

Bioinformatic Harvester http //harvester.embl.de/GenBank Brookhaven Protein Database ... 

When including pair correlation 61,0% of the residues were correctly predicted in a 3 state model and 51,9% in a 4 state model. The database encompassed 74 proteins from the Brookhaven Protein Data Bank. 

For those interested in statistics, in September 1998, there were 7657 structures deposited in the Brookhaven Protein Database (http //www.pdb.bnl.gov). These are analyzed on the scop database (http //scop.mrc-lmb.cam.ac.uk) into 435 folds, 640 superfamilies, 948 families, and 14 903 domains. There are probably about 1000 different superfamilies.35... 

Initially, we attempted to build a 3-D homology model of the transmembrane regions of the human thrombin receptor from the structure of IBRD, which is available from the Brookhaven Protein Database. Unfortunately, the suboptimal placement of several amino acid side chains resulted in severe deviations from structural standards for membrane-bound receptors with a seven-helix bundle topology (Figure 2). For example, carboxylate and ammonium groups on amino acid side chains at a mid-helix location were directed into the membrane, rather than toward the inside of the helix bundle, and the hydrophobic packing between some helices was either poor or nonexistent. 

Quantum mechanics calculations are more expensive to carry out because they require considerable more computing power and time than molecular mechanics calculations. Consequently, molecular mechanics is the more useful source of the large structures of interest to the medicinal chemist and so this chapter will concentrate on this method. To save time and expense, structures are often built up using information obtained from databases, such as the Cambridge and Brookhaven databases. Information from databases may also be used to check the accuracy of the modelling technique. However, in all cases, the accuracy of the structures obtained will depend on the accuracy of the data used in their determination. Furthermore, it must be appreciated that the molecular models produced by computers are a caricature of reality that simply provide us with a useful picture for design and communication purposes. It is important to realize that we still do not know what molecules actually look like ... 

The prediction of the secondary structures can be made by the structure similarity search of PDB collection at the site. Several servers provide such prediction method. The Jpred, which aligns the query sequence against PDB library, can be accessed at http //jura.ebi.ac.uk 8888/index.html. To predict the secondary structures, however, check Bypass the current Brookhaven Protein Database box and then click Run Secondary Structure Prediction on the home page of Jped to open the query page (Figure 12.10). Upload the sequence file via browser or paste the query sequence into the sequence box. Enter your e-mail address (optional) and click the Run Secondary Structure Prediction button. The results with the consensus structures are returned either online (linked file) or via e-mail (if e-mail address is entered). 

Although all proteinogenic amino acids form predominantly anti peptide bonds, a search in the Brookhaven Protein Database revealed that approximately 6-7% of all X-prolyl peptide bonds are found in the syn conformation in the native state of proteins [8]. The reason for this relatively frequent occurrence of syn-prolyl peptide bonds lies in steric repulsion of the proline 3 protons and the adjacent N-terminal amino acid in the anti conformation, resulting in a low barrier of rotation and energetically similar syn and anti isomers (Figure 1.2.3). 

CML is the best known of the XML notations for capture of structural data, but several other formats use XML-based syntax. The Protein Data Bank (PDB) (http // www.wwpdb.org/) is the single worldwide repository for macromolecular structure data. A representation of the Brookhaven PDB is available in an XML format called PDBML (Westbrook et al. 2005). PDBML provides a way to export structures and information about them from a relational database. Another database that offers... 

D Ottavio, T.W. (1998). A Database of PET ventilation measurements (Phase I), US DOE Contract No. DE-AC02-76CH00016, Brookhaven National Laboratories, Upton, New York. 

Biopolymer structnres are stored at the Protein Data Bank (PDB), founded in 1971 at Brookhaven National Laboratory (USA), and the Nucleic Acid Database (NDP), both currently operated by Rutgers, the State University of New Jersey (USA). As of April 2004, the PDB contained 25 176 structures and NDP had 2379 structures. 

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