|
Welcome to the Peptide Library Design & Calculator tool presented by Sigma-Aldrich You may launch the Design Tool and view these instructions at the same time, or view only the reference charts.
This tool enables you to design overlapping peptide fragment libraries for your native protein of interest. Features of this calculator include 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).
You will enter into the design tool by clicking on the  button at the bottom right side of the tool.
Copy and paste the protein sequence of interest in the large text box labeled  . This field will accept only the 1-letter amino acid code, but is not case sensitive and will accept both upper and lower-case letters. Alternatively, you can type the protein sequence of interest in this field.
| Amino Acid |
3 letter code |
1 letter code |
| Alanine |
Ala |
A |
| Cysteine |
Cys |
C |
| Aspartic acid |
Asp |
D |
| Glutamic acid |
Glu |
E |
| Phenylalanine |
Phe |
F |
| Glycine |
Gly |
G |
| Histidine |
His |
H |
| Isoleucine |
Ile |
I |
| Lysine |
Lys |
K |
| Leucine |
Leu |
L |
| Methionine |
Met |
M |
| Asparagine |
Asn |
N |
| Proline |
Pro |
P |
| Glutamine |
Gln |
Q |
| Arginine |
Arg |
R |
| Serine |
Ser |
S |
| Threonine |
Thr |
T |
| Valine |
Val |
V |
| Tryptophan |
Trp |
W |
| Tyrosine |
Tyr |
Y |
Peptide Length: This critical consideration will determine the success of the peptide library design. A value from 6 to 20 amino acids should be chosen for this field.
Amino Acid Overlap: This value (from 1-20) determines the frame shift, or number of residues that the peptide sequence is shifted along the native protein sequence. A smaller overlap (i.e. 1 or 2) will ensure more chances for multiple epitope hits. A larger overlap (i.e. >6+) will require fewer peptides, however, presents the least chance for multiple epitope hits.
Please review the tables below for guidance in selecting the appropriate peptide length and amino acid overlap:
This section allows output customization of the peptide library sequences. You can select multiple items in this section for the same design calculation.
Colorize: This enhancement 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 difficulties of each peptide sequence, based upon the amino acid composition.
Stair Step: This feature 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:
Calculate Hydropathy: This numerical value predicts the solubility characteristic of the peptide sequence in aqueous solutions. The value presented is the weighted average based upon 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 and based on the RP-HPLC retention times of peptide model systems at pH 7 by Monera.
| Weighted average |
Peptide hydrophobicity classification |
Solubility |
| 1 to 2.25 |
Very hydrophobic |
Very difficult to dissolve |
| 0.6 to 0.9 |
Moderately hydrophobic |
Difficult to dissolve |
| 0.1 to 0.5 |
Hydrophobic |
Likely soluble |
| -0.6 to 0 |
Hydrophilic |
Soluble |
| -1 to –0.5 |
Very hydrophilic |
Very soluble |
Correlations between Fauchere & Pliska and Monera et al Hydrophobicity Scales are shown below:
Click  to generate the peptide library sequences based on the defined Sequence Parameters and Sequence Output. The total number of sequences generated will be shown at the bottom right of the screen.
Click  to export the sequences to another file (i.e. Microsoft Word, Excel, etc). The sequence format is automatically tab-delimited so all information will be placed as separate columns. After selecting , data is automatically copied and ready for pasting into your file type of choice. You will not be prompted that the sequence are ready for pasting.
To place an order using the output of the desgin tool, paste the sequences into the Microsoft Office Excel ordering template (116KB). This spreadsheet can be submitted to peptides@sial.com for order review and placement.
Click  to clear all protein sequence and design results from the tool. This will reset (clear) all data so that you can begin a new design or modify the Peptide Sequence Parameters and/or the Format Sequence Output parameters.
We hope you find this tool useful. This is the first version of the design tool and Sigma-Aldrich will continue to enhance and expand this tool.
If you have any questions or suggestions regarding this tool, please contact peptides@sial.com.
|
