ExPASy

The importance of this information on biochemical reactions is emphasized by the fact that an image of the poster is also accessible on the ExPASy seiwer [20]. However, for this purpose, the poster has only been scanned. The ExPASy server provides a static image of the information on this web site, augmented only by links to additional information. 

Biochemical Pathways, G. MichaJ, Ed., Spektrum Akademischer Verlag, Heidelberg, 1999. http //www.expasy.ch [211 http //www2.chemie.uni-erlangen. de/support/biopath/index.html ... 

TrEMBL http / / www.expasy.ch/sprst/sprst-top.html... 

ExPASy (Expert lYotein Analysis System) molecular biology server http //WWW. expasy. ch... 

The reactant is referred to as a substrate. Alternatively it may be a nutrient for the growth of cells or its main function may require being transformed into some desirable chemical. The cells select reactants that will be combined and molecules that may be decomposed by using enzymes. These are produced only by living organisms, and commercial enzymes are produced by bacteria. Enzymes operate under mild conditions of temperature and pH. A database of the various types of enzymes and functions can be assessed from the following web site http //www.expasy.ch/enzyme/. This site also provides information about enzymatic reactions. 

The aim of the fust dimension breadth is to reveal sequence-function relationships by comparing protein sequences by sequence similarity. Simple bioinformatic algorithms can be used to compare a pair of related proteins or for sequence similarity searches e.g., BLAST (Basic Local Alignment Search Tool). Improved algorithms allow multiple alignments of larger number of proteins and extraction of consensus sequence pattern and sequence profiles or structural templates, which can be related to some functions, see e.g., under http //www. expasy.ch/tools/ similarity. 

Besides sensitive methods for the analysis of proteins, bioinformatics is one of the key components of proteome research. This includes software to monitor and quantify the separation of complex samples, e.g., to analyze 2DE images. Web-based database search engines are available to compare experimentally measured peptide masses or sequence ions of protein digests with theoretical values of peptides derived from protein sequences. Websites for database searching with mass spectrometric data may be found at http //www.expasy.ch/tools, http //prospector.ucsf. edu/ and http //www.matrixscience.com. 

Gasteiger, E. Gattiker, A. Hoogland, C. Ivanyi, I. Appel, R. D. Bairoch, A. ExPASy The proteomics server for in-depth protein knowledge and analysis. Nucl. Acids Res. 2003,31, 3784-3788. 

FIGURE 1.1 A 2D-gel electrophoresis map of colorectal epithelia cells proteins from the SWISS- 2DPage database (entry CATD HUMAN, primary access number P07339) accessible from http //www.expasy.org/swiss-2dpage. 

Dondi, F., Bassi, A., Cavazzini, A., Pietrogrande, M.C. (1998). A quantitative theory of the statistical degree of peak overlapping in chromatography. Anal. Chem. 70, 766. Eckerskom, C., Strupat, K., Schleuder, D., Hochstrasser, D.F., Sanchez, J.-C., Lottspeich, F., Hillenkamp, F. (1997). Analysis of proteins by direct-scanning infrared-MALDI mass spectrometry after 2D-PAGE separation and electroblotting. Anal. Chem. 69, 2888. Expasy,http //www.expasy.ch. 

Guex, N., Diemand, A., Peitsch, M. C. and Schwede, T. Deep ViewSwissPdb Viewer. Basel Swiss Institute ofBioinformatics, 2001. Available on line at www.expasy.org/spdbv/. 

Schwede T., Diemand A., Guex N., and Peitsch M. C. (2000) Protein structure computing in the genomic era. Res. Microbiol. 151, 107-112. http //www.expasy.ch/swissmod/SWISS-MODEL.html. 

SwissProt (http //www.expasy.org/sprot), database established by the Swiss Institute of Bioinformatics, provides protein sequences with high level of annotation. Highly integrated with other protein databases. All data are verified manually. 

UniProt (http //www.expasy.uniprot.org), Universal Protein Resource. Created by joining the Swiss-Prot information, TrEMBL and PIR contains protein sequence and function. 

Prosite (http //www.expasy.org/prosite), database of protein domains, families, and functional sites. 

ExPASy Proteomics tools (http //expasy.org/tools/), tools and online programs for protein identification and characterization, similarity searches, pattern and profile searches, posttranslational modification prediction, topology prediction, primary structure analysis, or secondary and tertiary structure prediction. 

SPTR is distributed in three files sprot.dat.Z, trembl.dat.Z, and trembl new.dat.Z. These files are, as indicated by their Z extension, Unix compress format files, which, when decompressed, produce ASCII files in SWISS-PROT format. Three others files are also available (sprot.fas.Z, trembl.fas.Z, and trembl new.fas.Z), which are compressed fasta format sequence files that are useful for building the databases used by FASTA, BLAST, and other sequence similarity search programs. These files should not be used for other purposes, because all annotation is lost when using this format. The SPTR files are stored in the directory /pub/databases/sp tr nrdb on the EBI FTP server (ftp.ebi.ac.uk) and in the directory /databases/sp tr nrdb on the ExPASyFTP server (ftp. expasy.ch). 

There are many specialized protein sequence databases. Some of them are quite small and contain only a handful of entries others are wider in scope and larger in size. This section describes three examples of specialized protein sequence databases. As this category of databases is quite changeable, any list provided here would soon be outdated. However, under the URL http //www.expasy.ch/alinks.html Proteins is a www document that lists information sources for molecular biologists that is continually update. 

A large part of the success of a 2-D PAGE run is determined by careful sample preparation. This topic and several of the nuances of 2-D PAGE are outside the scope of this chapter. Those interested should consult References 77 to 85. See also www.expasy.ch and www.proteomeworkssystem.com and associated links. 

ExPASy (Expert Protein Analysis System, www.expasy.ch) or the National Centre for Biotechnology Information (NCBI, www.ncbi.nlm.gov) websites. Both websites provide bioinformatics tools, links to sequence databases and extensive bibliographic resources. As an example of the wealth of information available on individual enzymes, at the time of writing a search based on nitrilase in the Entrez protein section of NCBI will recover more than 10000 references to nitrilase enzyme amino acid sequences. These can be rapidly screened online by organism, and the individual entries will have links to amino acid and gene sequence, relevant literature and information on protein features (such as conserved domains). 

SWISS- www.expasy.ch/swissmod/SWISS-MODEL.html Peitsch (1996)... 

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