ExPASy Proteomic tools

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. 

Rather than using an amino acid sequence to search SWISS-PROT, AACompI-dent of ExPASy Proteomic tools (http //www.expasy.ch/tools/) uses the amino acid composition of an unknown protein to identify known proteins of the same composition. The program requires the desired amino acid composition, the pi and molecular weight of the protein (if known), the appropriate taxonomic class, and any special keywords. The user must select from one of six amino acid constellations that influence how the analysis is performed. For each sequence in the database, the algorithm computes a score based on the difference in compositions between the sequence and the query composition. The results, returned by e-mail, are organized as three ranked lists. Because the computed scores are a measure of difference, a score of zero implies that there is exact correspondence between the query compo-... 

PeptideMass (ExPASy Proteomic tools), which is designed for use in peptide mapping experiments, determines the cleavage products of a protein after exposure to a specific protease or chemical reagent. The enzymes and reagents available for cleavage via PeptideMass are trypsin, chymotrypsin, Lys C, cyanogen bromide, Arg C, Asp N, and Glu C. 

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

Figure 11,4. ExPASy Proteomic tools. ExPASy server provides various tools for proteomic analysis which can be accessed from ExPASy Proteomic tools. These tools (locals or hyperlinks) include Protein identification and characterization, Translation from DNA sequences to protein sequences. Similarity searches, Pattern and profile searches, Post-translational modification prediction, Primary structure analysis, Secondary structure prediction, Tertiary structure inference, Transmembrane region detection, and Sequence alignment.

An amino acid scale refers to a numerical value assigned to each amino acid such as polarity, hydrophobicity, accessible/buried area of the residue, and propensity to form secondary structures (e.g., amino acid parameter of AAIndex). For example, selecting (clicking) ProtScale from the list of ExPASy Proteomics tools opens the query page with a list of predefined amino acid scales. Paste the query... 

Figure 11.5. ProtScale (ExPASy Proteomic Tools) output of hydrophobicity parameter. The hydrophobicity profile of cod alcohol dehydrogenase is generated with ProtScale using Eisenberg hydrophobic scale. The individual values for the 20 amino acids used in the profile are also listed in the report.

A number of servers offer various methods to predict secondary structures of proteins. Secondary structure prediction of ExPASy Proteomic tools (http //... 

A number of Web sites offer services in the secondary structure predictions of proteins using different approaches with varied accuracy. The Secondary structure prediction of ExPASy Proteomic tools (http //www.expasy.ch/tools/) provides pointers to different Web servers for predicting secondary structures of proteins. The ProtScale of ExPASy Proteomic tools produces conformational profiles by plotting statistical scales of various parameters (e.g., Chou and Fasman s conformational propensities, Levitt s conformational parameters) against residue positions. 

The annotated amino acid sequence files normally provide information concerning the sites and types for post-translational modifications and functions. These descriptions can be found from Features line(s) in all of the three sequence formats, namely, PIR, GenPept, and Swiss-Prot. The ExPASy Proteomics tools (http //www.expasy. ch/tools/) provide numerous links for such services. 

The ProtSite search can be conducted at ScanProsite tool (selecting Scan a sequence for the occurrence of PROSITE patterns) of ExPASy Proteomic tools (http //www.expasy.ch/tools/scnpsite.html), or PPSearch of EBI (http //www2.ebi.ac. uk/ppsearch/) or ProfileScan server (http //www.isrec.isb-sib.ch/software/PFSCAN form.html). On the search form, paste the query sequence, select options (e.g., display in PPSearch and databases in ProfileScan) and click the Run/Start the Scan button. The search results are returned (after clicking SEView applet button in ProfileScan) with different outputs as shown in Figure 12.16. 

ExPASy, home ExPASy Proteomics tools Homology Search System of DDBJ... 

Compute pI/MW (ExPASy Proteomic tools) is a tool that calculates the isoelectric point and molecular weight of an input sequence. Molecular weights are calculated by the addition of the average isotopic mass of each amino acid in the sequence plus that of one water molecule. The sequence can be furnished by the user in PASTA format, or by... 

Expert Protein Analysis System (ExPASy) ExPASy Proteomic tools ... 

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