PEPscreen® Library Design Reference Tables

Welcome to the Peptide Library Design & Calculator tool presented by Sigma-Aldrich

You may launch the Design Tool and reference these tables at the same time, or view the full instructions for getting started.

The protein sequence of interest should use the following letter designations.

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

 

Table 1. Summary of the potential effects of the different combinations between peptide length and offset number.
 

Offset Short Peptide Sequence Long Peptide Sequence  
Short Offset Number 1. Large number of short peptides are synthesized
1. Large number of short peptides are synthesized
2. Short peptides are easier to synthesize and often result in higher purity 2. Long peptide are usually difficult to synthesize and may result in lower purity
3. More chances for multiple epitope hits 3. More chances for multiple epitope hits
Long Offset Number 1. Fewer peptides are synthesized
1. Fewer peptides are synthesized
2. Short peptides are easier to synthesize and often result in higher purity 2. Long peptide are usually difficult to synthesize and may result in lower purity
3. Least chances for multiple epitope hits 3. Least chances for multiple epitope hits

 

Table 2. Number of peptide sequences in a protein given a set of predefined parameter (Peptide length and amino acid offset number).
 

Length of Protein Length of Peptides in the Library
Amino Acid Offset Number Number of Peptides in the Library
100 9
12
15
18
3
4
5
6
32
23
18
15
200 9
12
15
18
3
4
5
6
65
48
38
32
400 9
12
15
18
3
4
5
6
132
98
78
65
600 9
12
15
18
3
4
5
6
198
148
118
98
800 9
12
15
18
3
4
5
6
265
198
158
132
1000 9
12
15
18
3
4
5
6
331
248
198
165


Hydropathy values presented are 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: