Biomolecular databases

The DR lines link SWISS-PROT to other biomolecular databases. SWISS-PROT is currently linked to 29 different databases. The preceding example shows links to 19 different entries in 6 different databases. The cross references allow users to navigate to linked databases to retrieve part or all of the related information. The format of a DR line, except for cross references to PROSITE (Hofmann et al., 1999), Pfam (Bateman et al., 1999), and the EMBL nucleotide sequence databases (Stoesser et al., 1999), is the following ... 

In order to carry out such tasks, we need to combine a wide variety of methods and data. Chapter 1 of Volume 2 (Thure Etzold et al.) describes a successful and widely used approach for linking the vastly growing variety of biomolecular databases. 

SWISS-PROT [25, http //www.expasy.org/sprot/] is a curated protein sequence database which provides a high level of annotation, such as the description of a protein s function, its domain structure, PTMs, conflicts between literature references and variants. It also provides a minimal level of redundancy, a high level of integration with other biomolecular databases, and an extensive external documentation. Created in 1986, it now includes more than 100 000 entries from more than 7000 different species. SWISS-PROT is available from more than 100 WWW servers world-wide and its main host is the ExPASy server. 

PROT database distinguishes itself from other protein databases by (i) the generous annotation information (ii) a minimal redundancy for a given protein sequence and (iii) the cross-reference with many other biomolecular databases. 

An important factor in the progress of bioinformatics has been the constant increase in computer speed and memory capacity of desktop computers and the increasing sophistication of data processing techniques. The computation power of common personal computers has increased within 12 years approximately 100-fold in processor speed, 250-fold in RAM memory space and 500-fold or more in hard disk space, while the price has nearly halved. This enables acquisition, transformation, visuahsation and interpretation of large amounts of data at a fraction of the cost compared to 12 years ago. Presently, bioanalytical databases are also growing quickly in size and many databases are directly accessible via the Internet One of the first chemical databases to be placed on the Internet was the Brookha-ven protein data bank, which contains very valuable three-dimensional structural data of proteins. The primary resource for proteomics is the ExPASy (Expert Protein Analysis System) database, which is dedicated to the analysis of protein sequences and structures and contains a rapidly growing index of 2D-gel electrophoresis maps. Some primary biomolecular database resources compiled from spectroscopic data are given in Tab. 14.1. 

Table 14.1 Overview of some major biomolecular databases on the internet. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

The experimental exploration and confirmation of protein functions are relatively slow processes and always require dedicated experiments. The analysis of protein-protein associations as such improved remarkably in quality and speed. This is accompanied by the creation of new databases that will reflect the network of interacting proteins (the Protein Function and Metabolic Pathway project, http //bioinformer.ebi. ac.uk 80/newsletter/archives/4/pfmp.html, and the Biomolecular Interaction Network Database project http //bioinfo.mshri.on.ca/ BIND/). These activities contribute to the idea that cellular mechanisms can be better understood when they are seen as a multicomponent networked process. 

Alfarano, C., Andrade, C.E., Anthony, R, Bahroos, N., Bajec, M., Bantoft, R, Betel, D., Bobechko, B., Boutilier, R, Burgess, E., et al, (2005) The Biomolecular Interaction Network Database and Related Tools 2005 Update. Nucl Acids Res, 33, D418 24. 

Proteins interact with each other in many different ways. These interactions may be structural, evolutionary, functional, sequence based, and metabolical. Life depends on such biomolecular interactions. Among all these interactions, structural ones are the simplest and easiest to investigate because they are the most definite. Therefore, the main goals of bioinformatics are to create and to maintain the databases of the biological information which may lead to better understanding of these interactions. 

Figure 1. A simplified plot of the distribution of molecules (symbols) in an idealized two-dimensional chemical property space. The upper plot (a) represents a database consisting of discrete sets of close analogues. The lower plot (b) represents the Optiverse library. (Adapted from ref. 4. Copyright 1996 The Society for Biomolecular Screening, Inc.).

Cresset Database, Cresset BioMolecular Discovery, Letchworth http //www. cressetbmd.com/technology5.html. 

So, multiple MD is a good tool to assess the stability of conformers short biomolecules (this was also seen for the related peptide Tyr-Thr-Gly-Pro [50]). Due to the long length of the equilibration phase of a biomolecular system in aqueous solution, multiple MD simulations cannot be used in a blind systematic manner on a large ensemble of conformations. But it is very informative on a selected set of conformers, which have been derived by knowledge based conformational searches. The limit of the multiple simulation size in explicit water is about 10 conformers. Database searches seen to be a very good tool to derive low energy conformers all the conformations found in the structural database were found to be at least 1% populated in the 33.6 ns of simulation. 

BIND Biomolecular Interaction Network Database http //www.blueprint.org/index.phtml7page = databases... 

Bioinformatics is a rapidly expanding field, involving the application of computer technology to the management of biological information. Here, only two of the key bioinformatics components related to biomolecular engineering, database and computer modeling, are discussed. 

Bader, G. D., I. Donaldson, C. Wolting, B. F. Ouellette, T. Pawson, C. W. Hogue. 2001. BIND—The Biomolecular Interaction Network Database. Nucleic Acids Res 29 242-5. 

Blueprint Resource for biomolecular data focused on public databases for small molecule/domain interactions http //www.blueprint.org/... 

Biomolecular Interaction Network Database (Toronto, Ontario, Canada), http // www.bind.ca. 

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