Brookhaven Protein Data Base

Figure 7.4 A subset consisting of a total of 75000 amino acids in available 3D structures in the Brookhaven Protein Data Base has been screened for secondary structural preferences. Three categories has been classified , and turn. In (A) the total count has been given. Note the different total abundance of the amino acids. In (B) the percentages are given (number of a selected amino acid in a given secondary structural category divided with the total count of that amino acid). The third column in each entry gives the % abundance of an amino...

In the subsequent discussion of the structural biology of the immunophilins, all three dimensional structures are from the Brookhaven Protein Data Base, unless otherwise noted. Accession numbers for all protein structures are given at the end of the chapter. All graphical analysis was done using the modeling program Sybyl and associated modules.178... 

Ala = alanine Asn = asparagine Asp = aspartic acid Gin = glutamine Glu = glutamic acid His = histidine He = isoleucine Leu = leucine Lys = lysine Met = methionine PDB = Brookhaven Protein Data Base Phe = phenylalanine rmsd = root mean square deviation SA = simulated annealing Val = valine. 

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... 

ACE = angiotensin converting enzyme BFGS optimization = Broyden-Fletcher-Goldfarb-Shanno optimization CFS search = conformationally flexible structure search CNS central nervous system CSD = Cambridge Structural Database PDB = Brookhaven Protein Data Bank SBDD = structure-based drug design. 

Figure 2 Energy in kcal mol vs. phi, psi values based on a survey of the Brookhaven Protein Data Bank and from the CHARMM22 empirical force field. The protein survey data was placed into 15° x 15° bins and converted to free energies based on a Boltzmann distribution. The CHARMM22 surface was obtained by optimizing all degrees of freedom except for the phi and psi dihedrals at 15° increments. Note the CHARMM22 ALAD surface should not be considered to be rigorously correct however, the number and location of the minima are consistent with ab initio calculations ...

Figure 8 On the left is displayed the shape and the conformation of methotrexate as it is bound at the active site of dihydrofolate reductase (extracted from the Brookhaven Protein Data Bank database). On the right is the image with the results of a shape-based search on the ACD database the top 20 hits are overlayed (commercially available compounds)...

The text has been substantially revised, many new examples incorporated and errors corrected. A substantial new chapter dealing with supramolecular chemistry has been incorporated. Once again, a deliberate decision was made to try to limit references to the secondary rather than the primary literature. Where structural data have been presented, the use of the files of the Cambridge Crystallographic Data Centre and the Brookhaven Protein Structure Data Base are gratefully acknowledged. 

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... 

The results of structure determinations provide the core of a data base of biological macromolecular structure applicable to further investigations. Currently, the Protein Data Bank at the Chemistry Department of Brookhaven National Laboratories has responsibility for archival storage and distribution of these rs-sults in the United States of America (27). Later in this paper we shall discuss howsystems might be designed to facilitate access to such a data base. 

At Brookhaven National Laboratory, New York, the Protein Data Bank (PDB) was established in 1971, and has become a repository for protein coordinates which are shared between scientists worldwide. The PDB is a very important tool and the basis for rational, stracture-based drug design -a prerequisite for the development of modern biopharmaceuticals. 

PDB The Protein Data Bank, originally compiled at Brookhaven National Laboratory and currently distributed from http //www.rcsb.org, contains X-ray diffraction and NMR-based structural data of macromolecular structures such as proteins, nucleic acids, and entire viruses. The PDB is the primary structural databank for the 3-D coordinates of macromolecules and freely accessible on-line. 

Atomic coordinates for both hen egg-white and human lysozymes were based on crystallographic structures determined by Blake etal. (32-36) and deposited in the Protein Data Bank (Brookhaven National Laboratory). The distribution of hydrophobic, polar, and charged atoms on the surface of the two proteins was analyzed by calculating... 

Two new computer-based resources were launched in the 1970s. One was the Cambridge Structural Database (CSD based in Cambridge, England), and the other was the Protein Data Bank (PDB then based at Brookhaven National Laboratory in New York). Computational chemists recognized that these compilations of 3-D molecular structures would prove very useful, especially as more pharmaceutically relevant compounds were deposited. The CSD was supported by subscribers including pharmaceutical companies. On the other hand, the PDB was supported by American taxpayers. 

---