Bioinformatics description

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. 

To improve this unsatisfying situation, many bioinformatics sites construct nonredundant databases from a number of component databases, or they use external nonredundant databases, e.g., OWL (Bleasby et al., 1994). Both strategies considerably improve the situation for the end user, but they require the time- and resource-consuming maintenance of multiple databases or the acceptance of a certain time lag between creation of an entry and its appearance in the nonredundant database. Furthermore, both strategies lead to a loss of information in the individual entry owing to the diversity of database formats. Whereas OWL preserves most information of an entry and some of its structure, the NRDB program requires a conversion of the component databases to FASTA format, which contains only one description line per entry. 

SWISS-PROT (Bairoch and Apweiler, 2000) is a protein sequence database that, from its inception in 1986, was produced collaboratively by the Department of Medical Biochemistry at the University of Geneva and the EMBL. The database is now maintained collaboratively by Swiss Institute of Bioinformatics (SIB) and EBI/EMBL. SWISS-PROT provides high-level annotations, including descriptions of the function of the protein and of the structure of its domains, its post-translational modifications, its variants, and so on. The database can be accessed from http //expasy.hcuge.ch/sprot/sprot-top.html or numerous mirror sites. In 1966, Translated EMBL (TrEMBL) was created as a computer-annotated supplement to SWISS-PROT (Bleasby et al, 1994). 

As mentioned in Chapter 2 for the description of our Y2H library screening procedure, what we obtained after a bioinformatics analysis is the location of the interacting domain within the bait or the prey protein. In reality, we do not measure interaction between full length proteins but between domains within proteins which is a closer representation of an in vivo interaction where only some key fragments of each protein interact with one another in space. These domains were called Selected Interacting Domain or SID. It is therefore clear that bioinformatics sequence analysis that compare SIDs obtained from Y2H experiments with Interpro domains can lead to very interesting observation regarding the domain keen to interact and can help to discriminate more specifically true and false positives. 

This broad description of bioinformatics and of the two types of bioinformatics scientist is quite abstract. It does not detail the characteristics of the data with which the bioinformatics scientist has to work. Neither does it define the set of tools that the developer should work with or implement. There was a time, in the late 1980s and early 1990s, when the type of data was well defined. Molecular sequence data, the stream of bases in DNA, and the stream of residues at the protein level vvoe the main types of data. Programmers developed code in FORTRAN or C and scripting languages were immature. 

The ENZYME database1501, maintained by the Swiss Institute for Bioinformatics (SIB), provides a comprehensive list of all IUBMB classifications, together with associated information such as systematic and alternative enzyme names, cofactor requirements, and pointers to the corresponding entry in the SWISS-PROT database of protein sequences1511. In addition, there is a concise free-text description of the reaction catalyzed, together with a description of preferential substrates and products. Currently, the ENZYME database holds entries for approximately 3700 enzymes. 

Xie, L. and Bourne, P. E. 2007. A robust and efficient algorithm for the shape description of protein structures and its apipUcation in predicting ligand binding sites. BMC Bioinformatics 8 Suppl 4 S9. 

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