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...

PDB is one of the oldest protein data bases, founded in 1971. It has three locations, Rutgers University in New Jersey, San Diego Supercomputer Center (SDSC) at the University of California, and the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland. The PDB is a source for protein characterization and structure as well. The PDB archive contains macromolecular structure data on proteins, nucleic acids, protein-nucleic acid complexes, and viruses. Approximately 50-100 new structures are deposited each week, which are annotated and released upon the depositor s specifications. PDB data are freely available worldwide. PDB formats, annotates, validates, and releases dozens of complicated structure files each week some of them take only a couple of hours, others take weeks to process. Data processing is the main task of people at the PDB and validation is the most time-consuming part (Smith-Schmidt, 2002). 

Tertiary Structure of Proteins The tertiary structure of a protein refers to how the alpha helices and beta sheet portions of a polypeptide chain are folded into a compact or globular structure. Two-dimensional representations of the three-dimensional tertiary structures of proteins are, well, pretty two dimensional. If you want to better understand tertiary structure, you can view interactive, three-dimensional models of a large variety of proteins at the RCSB Protein Data Base at http //www.rcsb.org. 

Amino acid sequencing and searching in protein data bases Bioinformatics (BLAST program) (http //www.ncbi.nlm.nih.gov)... 

Experimental structures are often the basis for computational studies they are used as input structures for structure optimizations and conformational searches, for the parameterization and validation of force fields and for analyzing the effects of crystal lattices. More than 200,000 experimental structures have been reported, and the majority are found in the Cambridge Structural Data Base (CSD, small molecular structures which include carbon atoms) the Inorganic Crystals Structure Database (ICSD) and the Protein Data Base (PDB this database includes X-ray as well as optimized structures based on NMR data). 

Protein structure taken from the RSCB Protein Data Base and modified ... 

In the case of the fluorescein-binding variant FluA, crystals were obtained in the presence of the hgand at pH 8.1 with two FluA fluorescein complexes in the asymmetric unit, which were refined to a resolution of 2.0 A [52]. The two molecules were highly similar in structure, with a root mean square difference (rmsd) of 0.33 A for 173 mutually superimposed positions. The overall topology of the //-barrel with the a-hehx attached to it, both of which are characteristic features of the lipocahn architecture (see Section 8.2), was found to be conserved (Fig. 8.4). Both disulfide bonds of the BBP scaffold, one between Cys and fJys and one between Cys" and Cys, were also clearly visible. Upon superposition with the BBP crystal structure (molecule A from the Protein Data Base entry IBBP [32]), an rmsd of 1.2 A was calculated for 159 superimposed positions. 

Although originally defined for the conformation adopted by polymers of proline, the PPII helical conformation can be adopted by amino acid sequences other than those based on proline. This was noticed during several statistical surveys of structures in the Protein Data Base (PDB), which estimated that up to 10% of residues that are not assigned to a regular secondary structure have PPII dihedral angles but contain little proline (Sreerama and Woody, 1994). 

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... 

Our objective is to develop analytical systems and protein data bases for agricultural products which allow proteins to be identified with confidence by position, to identify as many "known" proteins as possible in the patterns, and to develop methods for quickly and reliably finding both quantitative and qualitative differences... 

Figure 4.4. Schematic representation of rat CPR domains (protein data base [pdb] code lAMO). In the crystal, the two flavins, FMN and FAD, are 4 A apart.

Selecting protein data bases for training and for testing... 

Both training and testing process take only several minutes on the PC equipped with the 486 processor in the case when up to 200 proteins are used. The FORTRAN source code, files with Gaussian parameters and protein data bases used in this report are available via Internet (see Supplementary Material). 

Cross-validation, overtraining and sensitivity to the choice of protein data base... 

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