Proteins data bank

As a template for an intermediate conformation of protein kinase, the crystal structure of the binary complex of cAPK with adenosine (Ibkx.pdb in the Protein Data Bank) was used. As templates for open conformations... 

Preparation of a Brookhaven Protein Data Bank (PDB)-formatted [10] file containing the coordinates and appropriate names of all atoms, including all polar and aromatic hydrogens. 

To find appropriate empirical pair potentials from the known protein structures in the Brookhaven Protein Data Bank, it is necessary to calculate densities for the distance distribution of Ga-atoms at given bond distance d and given residue assignments ai,a2- Up to a constant factor that is immaterial for subsequent structure determination by global optimization, the potentials then ciiiergo as the negative logarithm of the densities. Since... 

We tested our new potential by applying a local optimization procedure to the potential of some proteins, starting with the native structure as given in the Brookhaven Protein Data Bank, and observing how far the coordinates moved through local optimization. For a good potential, one expects the optimizer to be close to the native structure. As in Ulrich et al. [34], we measure the distance between optimizer B and native structure A by the distance matrix error... 

F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E. Meyer, M.D. Bryce, J.R. Rogers, O. Kennard, T. Shikanouchi and M. Tasumi, The protein data bank A computer-based archival file for macromolecular structures, J. Mol. Biol. 112 (1977), 535-542. 

D.R. Stampf, C.E. Felser and J.L. Sussman, PDBBrowse - a graphics interface to the Brookhaven Protein Data Bank, Nature 374 (1995), 572-574. 

L.L. Walsh, Navigating the Brookhaven Protein Data Bank, Gabos Communication 10 (1994), 551-557. 

PDB file. pdb Protein Data Bank file format for 3D stmcture information on proteins and polynucleotides nmm.rcsb.org 53... 

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. 

Having looked at the general structure of PDB files, let us now examine a sample PDB file. The file represents the structure of r conotoxin PNll polypeptide (PDB ID Ipcn) and was retrieved from the Protein Data Bank [53]. Figure 2-109 shows the 3D structure of the molecule. 

The fir.-fit line of the file (see Figure 2-110) - the HEADER record - hold.s the moleculc. s classification string (columns 11-50), the deposition date (the date when the data were received by the PDB) in columns 51-59, and the PDB (Dcode for the molecule, which is unique within the Protein Data Bank, in columns 63-66. The second line - the TITLE record - contains the title of the experiment or the analysis that is represented in the entry. The subsequent records contain a more detailed description of the macromolecular content of the entiy (COMPND), the biological and/or chemical source ofeach biological molecule in the entiy (SOURCE), a set ofkeywords relevant to the entiy (KEYWDS). information about the experiment (EXPDTA), a list of people responsible for the contents of this entiy (.AUTHOR), a history of modifications made to this entiy since its release (REVDAT), and finally the primaiy literature citation that describes the experiment which resulted in the deposited dataset ()RNL). 

As this short example shows. PDB files use different syntax for different records and both writing and reading such files require much effort. Another problem is the extensibility of this format to handle new kinds of information, which further complicates the file structure. The Protein Data Bank has been faced with the consequences - the existing legacy data comply with several different PDB formats, so they are not uniform and they arc more difEcuh to handle (145, 155, 157]. As mentioned in Section 2,9.7.1, there is a much more flexible and general way of representing molecular structure codes and associated information - the STAR file format and the file formats based on it. 

D structures of macromolecules, especially proteins and nudeic adds, are found in the Protein Data Bank (PDB) [27]. 

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, NRL3D Protein Data Bank - protein structures (mostly fror X-ray crystallography). NRL3D is a derived sequence database in PIR format... 

Bernstein F C, T F Koetzle, G J B Williams, E Meyer, M D Bryce, J R Rogers, O Kennard, T Shikanouchi and M Tasumi 1977. The Protein Data Bank A Computer-Based Archival File for Macromolecular Structures. Journal of Molecular Biology 112 535-542. 

Protein Data Bank (Section 27 20) A central repository in which crystallographic coordinates for biological mole cules especially proteins are stored The data are accessi ble via the Worldwide Web and can be transformed into three dimensional images with appropriate molecular modeling software... 

The Protein Data Bank PDB ID 1A71 Colby T D Bahnson B J Chin J K Klinman J P Goldstein B M Active Site Modifications m a Double Mutant of Liver Alcohol Dehydrogenase Structural Studies of Two Enzyme Ligand Com plexes To be published... 

Page 1093 (Figure 26 9c) is adapted from crystallographic coordinates deposited with the Protein Data Bank PDB ID ICLE Ghosh D Wawrzak Z Pletnev V Z Li N Kaiser R Pangbom W Jornvall H Erman M Duax W L Structure of Un complexed and Linoleate Bound Candida Cholesterol Esterase To be published... 

Page 1171 (Figure 28 7) is adapted from crystallograpliic coordinates deposited with The Protein Data Bank PDB ID lAOl Luger A Mader W Richmond R K Sargent D F Richmond T J Crystal Structure of the Nucleosome Core Particle at 2 8 A Resolution Nature 1997 V 389 251... 

HyperChem residue templates. HyperChem uses these templates when it reads a Protein Data Bank file or when you construct a molecule from residues. 

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

Fig. 3. Representation of the nine principal folds which recur in protein stmctures, where the codes of the representative proteins taken from the Brookhaven Protein Data Bank (PDB) (17) are given in parentheses (18) (1) globin (Ithb) (2) trefoil (lilb) (3) up—down (256b) (4) immunoglobulin folds...

EE Abola, EC Bernstein, SH Bryant, TF Koetzle, J Weng. Protein data bank. In EH Allen, G Bergerhoff, R Sievers, eds. Crystallographic Databases Information, Content, Software Systems, Scientific Applications, Bonn Data Commission of the International Union of Crystallography, 1987, pp 107-132. 

PC Bernstein, TP Koetzle, GIB Williams, EE Meyer, MD Brice, JR Rodgers, O Kennard, T Shimanouchi, M Tasumi. Protein Data Bank Computer based archival file for macromolecular structure. J Mol Biol 112 535-542, 1977. 

Software for structure determination and analysis at the Protein Data Bank http //www.rcsb.org/pdb/Modeling... 

The first requirement for threading is to have a database of all the known different protein folds. Eisenberg has used his own library of about 800 folds, which represents a minimally redundant set of the more than 6000 structures deposited at the Protein Data Bank. Other groups use databases available on the World Wide Web, where the folds are hierarchically ordered according to structural and functional similarities, such as SCOP, designed by Alexey Murzin and Cyrus Chothia in Cambridge, UK. 

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