Protein information resource description

The Protein Information Resources (PIR) (Wu et al., 2002) of NBRF in collaboration with MIPS and JIPID produces the annotated protein sequence database in the PIR-MIPS International Protein Sequence Database (PSD). The PSD is a comprehensive annotated and nonredundant protein sequence database. Its annotation includes concurrent cross-references to other sequence, structure, genomic and citatation databases, as well as functional descriptions and structural features. The PIR-International database is accessible at the PIR site, http //pir, georgetown.edu, and at the MIPS site, http //www.mips.biochem.mpg.de. 

As with the DE lines, the CC lines give an indication about the level of characterization of a protein. The example provides experimentally verified information about the "function", the quatenary structure ("SUBUNIT"), the "SUBCELLULAR LOCATION" and the "TISSUE SPECIFICITY" of the protein. A description of the "disease (s) " known to be associated with a deficiency of the protein, a description of the "SIMILARITY" of the protein with other proteins, and a cross reference to network "DATABASE" resource(s) for this specific protein are also found. 

Alternatively, some concepts may be described in more detail, approaching a near textbook-like description. Colored illustrations may be used and textbooks may be cited, if they were used as resources for this information. For example, Hergenrother includes an introduction to apoptosis in his proposal, using both text and graphics. A short passage from his text is reproduced in excerpt 12F, where he describes how either underactive or overactive apop-totic processes can lead to dire cellular consequences. Understanding apop-totic processes is important to his proposed work, which involves apoptotic proteins. 

Our discussion of globular protein structure begins with the principles gleaned from the earliest protein structures to be elucidated. This is followed by a detailed description of protein substructure and comparative categorization. Such discussions are possible only because of the vast amount of information available over the Internet from resources such as the Protein Data Bank (PDB www.rcsb.org/pdb), an archive of experimentally determined three-dimensional structures of biological macromolecules. 

This Section briefly describes the data resources available and relevant for researchers working in proteomics. The databases can be classified according to the type of information provided, i.e. protein sequence, nucleotide sequence, pattern/profile, 2-DE, 3-D structure, PTM, genomic, and metabolic. A more extensive description and list has been published by Bairoch [55], A reasonably exhaustive and constantly updated list of databases can also be found at http //www.expasy.org/alinks.html. Here we focus on sequence databases, protein domain databases, 2-D PAGE, and PTM databases. 

A comprehensive description of the databases and methods for domain, family, and pattern identification is available in chapter 2. Therefore, in this chapter, the discussion of the application of family and domain information to function assignment will be limited to Pfam, the virtual standard in protein domain/family classification, and to InterPro and CDD, two resources that integrate multiple domain databases. In addition, I discuss tools that can be used to scan those databases, namely HMMER,... 

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