ProtScale tool

ProtScale tool of ExPASy computes amino acid scale (physicochemical properties/parameters) and presents the result in a profile plot. Perform ProtScale computations to compare the hydrophobicity/polarity profiles with %buried resi-dues/%accessible residues profiles for human serine protease with the following amino acid sequence. 

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. 

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 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. 

ProtScale (http //www.expasy.org/tools/protscale.html)... 

The ExPASy Proteomic Server (http //www.expasy.org) or its mirror site (e.g. http //us.expasy.org in U.S.A. and http //ca.expay.org in Canada) provides comprehensive resources and tools for proteomic analyses. They include Databases (e.g. Swiss-Prot, Prosite, Enzyme), Tools (e.g. BLAST, ProtParam, ProtScale, SIM, SWISS-MODEL, Translate), Services (e.g. ExPASy ftp server, BioHunt, 2D Hunt), Documentation and links. 

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