Expert Protein Analysis System ExPASy

Swiss-Prot and TrEMBL are the initial databases one would use to find information regarding the protein s sequence. Depending on the level of refinement and information provided for each sequence, data are deposited into either Swiss-Prot or TrEMBL. Because of the large number of sequences that are now determined from genomics alone, all sequences are first deposited into TrEMBL. Once the correct nomenclature, links to relevant databases, and significant comments are added, and after unnecessary information has been removed, the sequence is added to the Swiss-Prot database. The initial search for a sequence is typically performed on the information contained in these two databases. 

The PROSITE database is used to determine the domain and the family of the protein sequences that, in turn, are based on biologically significant sites, patterns, and profiles.This database is similar to the HOMologous STRucture Alignment Database (HOMSTRAD) and the Protein family (Pfam) database, both of which contain domain and family information for proteins. HOMSTRAD uses sequence and structure to group proteins into domains and families. Pfam classifies protein domains and families, based 

The results of these tests are displayed as bar graphs, where positive values indicate misaligned or misfolded regions and negative values indicate 

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A number of useful computational tools have been developed for predicting the identity of unknown proteins based on the physical and chemical properties of amino acids and vice versa. Many of these tools are available through the Expert Protein Analysis System (ExPASy) at http //www.expasy.ch (Appel et al., 1994) and other servers. 

Expert Protein Analysis System (ExPASy) GenBank Google... 

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). 

Expert Protein Analysis System http //expasy.hcuge.ch/... 

The ENZYME nomenclature database (Figure 7.3) of ExPASy (Expert Protein Analysis System) at http //www.expasy.ch/enzyme/ can be searched by entering EC number or enzyme names. The query returns information on EC number, enzyme name, catalytic activity, cofactors (if any) and pointers to Swiss-Prot sequence, ProSite, and human disease(s) of the enzyme deficiency. 

The comprehensive molecular biology server, ExPASy (Expert Protein Analysis System), provides Proteomic tools (http //www.expasy.ch/tools) that can be accessed directly or from the ExPASy home page by selecting Identification and Characterization under Tools and Software Packages. The Protein identification and characterization tools of the Proteomics tools (Figure 11.4) provide facilities to ... 

The ExPASy (Expert Protein Analysis System, http //www.expasy.ch/) proteomics server of the Swiss Institute of Bioinformatics, P05790. 

The CMS Molecular Biology Resource [168] at the San Diego Supercomputer Center contains an excellent compendium of Web-accessible bioinformatics tools. The ExPASy (Expert Protein Analysis System] proteomics server of the Swiss Institute of Bioinformatics [169] and the EBI Toolbox are two other popular tool collections. Another useful resource is Herbert Mayer s Bioinformatics World Web site, which contains a comprehensive collection of bioinformatics tools and software, including evaluations, comments, and tutorials. 

Results of structure prediction using the methods discussed in this section are available on the Web as well. One of the most useful URLs is http // predictioncenter.gc.ucdavis.edu. Other excellent sources of information are available through the National Institutes of Health (http //pubmedcentral.nih. gov/tocrender.fcgi iid=1005 and http //www.ncbi.nlm.nih.gov), and through the ExPASy (Expert Protein Analysis System) server (http //us.expasy.org). 

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. 

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