Databases Protein Data Bank

PIR-International Protein Sequence Database Protein Data Bank (PDB) ... 

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). 

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

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

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. 

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. 

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. 

Nomenclature resources help the user give correct names to chemical structures. Visualization resources allow the user to build molecules from scratch or display molecular structures imported from databases or other software programs (like the Protein Data Bank, PDB, for example). 

Abola EE, Bernstein FC, Bryant SH, Koetzle TF,Weng J (1987) In Allen FH, Bergerhoff G, Sievers R (eds) Protein data bank in crystaUographic databases-information content, software systems, scientific applications. Data Commission of the International Union of Crystallography, Bonn Cambridge Chester, pp 107-132... 

I wish to thank Andrew B. Carrell, who assisted with many of the calculations and figure preparations necessary for the production of this chapter. I also thank H. L. Carrell, G. D. Markham, A. S. Mildvan, and E. K. Patterson for many helpful discussions. Ball-and-stick drawings were drawn with the computer program VIEW (Carrell, 1976). Use of the Cambridge Structural Database (Allen etal., 1979) and the Protein Data Bank (Bernstein el al., 1977) is acknowledged. This work was supported by National Institutes of Health grants GM 44360, CA 10925, and CA 06927 and by an appropriation from the Commonwealth of Pennsylvania. 

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. 

The X-ray crystal structures shown in this article were created with CambridgeSoft s ChemSD Pro 5.0 using coordinates obtained from the source, the CSD (Cambridge Structural Database) or the PDB (Protein Data Bank), or those determined by Paul D. Robinson at Southern Illinois University (SIU) in collaboration with the author. Most of the author s work on boron heterocycles first at SIU and more recently at SRI International (the nonprofit research institute formerly known as the Stanford Research Institute) was funded by NIH grant GM448I9. 

Kinase protein/ligand crystal complexes were retrieved from the Pfizer Crystal Structure Database, an in-house X-ray structure repository that contains internally solved structures and selected ones imported from the Protein Data Bank (1). Kinase assay data were obtained by querying against Pfizer screening database for screens associated with any kinase target and tagged with IC50 or ICi as the endpoint type. 

FIGURE 4-22 Organization of proteins based on motifs. Shown here are just a small number of the hundreds of known stable motifs. They are divided into four classes all a, all /3, all3, and a + /3. Structural classification data from the SCOP (Structural Classification of Proteins) database (http //scop.mrc-lmb.cam.ac.uk/scop) are also provided. The PDB identifier is the unique number given to each structure archived in the Protein Data Bank (www.rcsb.org/pdb). The a//3 barrel, shown in Figure 4-21, is another particularly common a/fS motif. 

Lysozyme and Antibodies To fully appreciate how proteins function in a cell, it is helpful to have a three-dimensional view of how proteins interact with other cellular components. Fortunately, this is possible using on-line protein databases and the three-dimensional molecular viewing utilities Chime and Protein Explorer. If you have not yet installed the Chime plug-in on your computer, go to www.mdlchime.com/chime and follow the instructions for your operating system and browser. Once chime is installed, go to the Protein Data Bank (www.rcsb.org/pdb). 

The x,y,z coordinates of all atoms in published, refined three-dimensional structures have been deposited in the Protein Data Bank (Table 3-4).568 571 Many other related databases are available,572 e.g., covering molecular modeling,573 gene sequences, proteome data,574 and much, much more. A good way to keep up to date is to read the "computer comer" in Trends in Biochemical Sciences (TIBS). Most databases can be reached on the World Wide Web.572 A selected list is... 

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