Brookhaven Protein Database

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

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. 

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). 

In contrast to typical expert systems, ARC is written in C-h- and includes a rules base in binary format, which can be created with information from different file formats, such as MDL Molfile, Brookhaven Protein Database, Gasteiger Cleartext, JCAMP (DX, JDX, JCM, and CS), binary files (molecule sets, databases, code... 

In folded proteins the conformational state of a prolyl bond is usually well defined, because in most cases only one of the two conformations (cis or trans) can be accommodated in the folded structure. Of 1435 nonredundant protein structures in the Brookhaven protein database, 43% contain at least one cis peptidyl-prolyl bond (Reimer et al., 1998), and 7% of all prolyl peptide bonds in folded proteins are cis (Stewart et al., 1990 Macarthur and Thornton, 1991). 

FIGURE 5 View of the a-carbon backbone of calmodulin (blue) bound to calmodulin binding domain peptide (red) of smooth muscle MLCK. This view is derived from the crystal structure (Meador et al, 1992) as deposited in the Brookhaven Protein Database (reference number ICDL). The peptide includes hydrophobic residues (yellow), Trp and Leu, at its N and C termini, respectively. 

PDB - protein database format, the original format of the Brookhaven protein database. A format used to store crystallographic and modeling information about proteins. It should be avoided when storing anything else due to its extremely ambiguous coding scheme. ... 

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). 

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

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. 

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... 

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. 

In order to establish a set of realistic aqueous solution conformations for the peptide Ala-Pro-Tyr, cartesian coordinates from the Brookhaven Protein Data Bank (PDB), the SCAN3D database [35], (a representative set of non-homologous high-resolution protein crystal structures selected from the PDB), and from the Cambridge Crystal Structure Database (CSD) were used. 

PSSD is a database that incorporates sequences of secondary-structure elements for all proteins with three-dimensional structures defined by experimental methods (such as NMR-Spectroscopy or X-Ray Crystallography) and for which structural data exist in the Brookhaven protein databank. 

Templates can be selected using the target sequence as a query for searching protein structure databases [e.g. Brookhaven Protein Data Bank (PDB) http / /www.rcsb.org/pdb/index.html Structural Classification of Proteins (SCOP) scop.mrc-lmb.cam.ac.uk/scop/ DALI www2.ebi.ac.uk/dali/ Class, Architecture, Topology and Homologous superfamily classification at CATH www.biochem.ucl.a-c.uk/bsm/cath/). 

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