Total 36 physiochemical properties (parameters) of amino acid sequence are used in this server. These parameters were obtained from literature (Hofman, K. and W. Stoffel. 1992). Broadly these parameters can be divided in following categories.
Hydrophobicity/Hydrophilicity: Hydrophobicity or Hydrophilicity plots provide clues to the tertiary structure of proteins (Bangham, 1988; Chothia 1984). These parameter help in identifying the transmembrane helices. In this study we included 13 parameters/tables, obtained from literature.
Flexibility: The flexibility is a crucial property of proteins. It helps the users in identifying the region in protein, which have high potential for turn. Their functional and structural features depend on various kind of motion (Facchiano, 1989). The flexibility plot of a protein lies on observation that aminoacid residues with the highest turn potential i.e. located in highly mobile regions of protein surface. We included 5 type of tables in this server, in order to calculate various aspects of flexibility (e.g. local flexibility, flexibility with rigid neighbor).
Accessible Surface Area: This parameter is very useful in detecting the region that is accessible. This are is usually found at surface of protein. For example if you are looking binding region in your protein that binds to another protein, than above parameter may provide clue, because binding region is found on surface. Thus parameter ‘Accessible Surface Area’ plot can help you in identifying region of in protein, which are accessible. In this server, we provide 7 tables obtained from literature.
Charge/Polarity: Charge residue or segment of residues provide clue about function of protein. In this study four tables have been included.
Miscellenious Parameters: This server also allow to plot various parameters like volume, refrectivity, OMH, free transfer energy etc.
Related References
1. Barton G. J. 1990. Protein multiple sequence alignment and flexible pattern matching. Methods in Enzmol. 183: 403-428.
2. Barton, G. J. 1993. ALSCRIPT a tool to format multiple sequence alignments. Protein Eng., 6, 37-40.
3. Gouet, P., E. Courcelle, D. I. Stuart, and F. Metoz. 1999. ESPript: analysis of multiple sequence alignment in PostScript. Bioinformatics 15: 05-308.
4. Hofman, K. and W. Stoffel. 1992. PROFILEGRAPH: An interactive graphical tool for protein sequence analysis. Comput. Applic. Biosci. 8: 331-337.
5. Kyte, J. and R. F. Doolittle. 1982. A simple method for displaying hydrophobic character of protein. J. Mol. Biol. 157: 105-132.
6. Livingstone, C. L. and G. J. Barton. 1993. Protein sequence alignments: a strategy for the hierarchial analysis of residue conservation. Comput. Applic. Biosci. 9, 745-756.
7. Nihalani, D., G. P. S. Raghava, and G. Sahni. 1997. Mapping of the plasminogen binding site of streptokinase with short synthetic peptides. Protein Science 6: 1284-92.
8. Ponnuswamy, P. K., M. Prabhakran and P. Manavalan. 1980. Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins. Biochem. Biophys. Acta, 623: 301-316.
9. Raghava, G.P.S., and G. Sahni. 1994. GMAP: a multipurpose computer program to aid synthetic gene design, cassette mutagenesis and introduction of potential restriction sites into DNA sequences. Biotechniques 16: 1116-1123.
10. Thompson, J. D., D. G. Higgins and T. J. Gibson. 1994. CLUSTAL-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22: 4673-80.
11. Wilkins M.R., E. Gasteiger, A. Bairoch, J.-C. Sanchez, K. L. Williams, R. D. Appel, D. F. Hochstrasser.1998. Protein identification and analysis tools in the ExPASy server in: 2-D Proteome Analysis Protocols. Editor A.J. Link. Humana Press, New Jersey.