You may launch the Design Tool and view these instructions at the same time, or view only the reference charts.
Design overlapping peptide fragment libraries for your native protein of interest. Features of this peptide library design tool includes the ability to set custom sequence parameters (peptide length and amino acid offset), format the sequence output and export the custom peptide library sequences to other programs (Microsoft Word, Excel, etc).
a) Colorize: This option will visually display, by color representation, the hydrophobic classification of each amino acid within the peptide sequence. This allows you to visually determine potential synthesis and/or solubilization difficulties of each peptide sequence, based upon the amino acid composition.
b) Stair Step: This option displays the peptide library sequences by the amino acid overlap as determined in the Sequence Parameters. Potentially missed epitopes can be quickly determined based on this format, as you are able to easily see the amino acid overlap relative to neighboring sequences. Example Protein Sequence: AVHNDTMTFRAPHSTWSEISILLQEVGSLGLSGDLRCGQRSQESP Calculated peptide sequences based on a peptide length of 15 and amino acid overlap of 5:
c) Calculate Hydropathy: This numerical value predicts the solubility characteristic of the peptide sequence in aqueous solutions. The value presented is based upon the weighted average known hydropathy values per amino acid divided by the length of the peptide sequence. The values are based on model systems of free energy transfer of acetyl-amino acyl amides (Ac-AA-am) by Fauchere & Pliska (1988) and based on the RP-HPLC retention times of peptide model systems at pH 7 by Monera.
Correlations between Fauchere & Pliska and Monera et al Hydrophobicity Scales are shown below:
If you have any questions or suggestions regarding this tool, please contact peptides@sial.com.
如要继续阅读,请登录或创建帐户。
暂无帐户?