1. Click on the desire module.
2. Input the number of residues of peptide you want to build.
3. At each position select the type of amino acid you want for particular position in a peptide chain.
4. Click on Submit and wait for few minutes for result to load on your browser.

Total number of Combinations of sequence will appear along with other physiological parameters listed below

Molecular weight of each peptide will be displayed on screen.

Charge of Peptide
Net charge on peptide depends on the number of charged amino acids it contains and the pH of its environment. The isoelectric point is the point at which net charge zero. There is different dissociation constant, KD of each amino acid. At physiological pHs the amino acids which can be ionized are: aspartate (D), glutamate (E), lysine (K), arginine (R), and histidine (H). Also, the N and C terminus can be ionized.[2]

Solubility
Working with peptides is to determine the suitable solvent in which it can dissolve. Some peptides can easily dissolve in aqueous solutions but common problem encountered is low solubility or insolubility, especially with peptides having long sequences of hydrophobic amino acids. Physiochemical characteristics of each amino acid can help to predict the peptide’s solubility.[3]

Peptides that contains a high proportion (> 75%) of D, E, H, K, N, Q, R, S, T, Y are capable of establishing intermolecular hydrogen bonds (i.e., crosslinking), thus forming gels in aqueous solutions.

Peptides which have 50% or more hydrophobic residues might be insoluble or partly soluble in aqueous solutions.

Hydropathy Index
The Hydropathy index is a number representing the hydrophobic or hydrophilic properties of amino acid sidechain. It was proposed by Jack Kyte and Russell F. Doolittle in 1982.[4]

The large peptides exhibit more hydrophobicity. Isoleucine (4.5) and valine (4.2) are the most hydrophobic amino acids while arginine (-4.5) and lysine (-3.9) have more hydrophilic character. It is very important in protein structure; hydrophobic amino acids tend to be internal (with regard to the protein's tertiary structure) while hydrophilic amino acids are mostly existing towards the protein surface.

Isoelectric Point (IPC Peptide)
The point at which the overall net charge of the peptide is zero i.e. a neutral charge. Separation of proteins at the isoelectric point is called isoelectric focusing. Separation is done on the basis of the positive or negative groups present on the molecule.[5]

Model
Model of particular peptide can be visualized by clicking on corresponding model tab. The model can also be downloaded.

1. Amino acid reference, Properties of Common Amino Acids, https://www.sigmaaldrich.com/life-science/metabolomics.html(accessed 15 October 2018).
2. Lehninger, A. L., Nelson, D. L. 1., & Cox, M. M. (2008). Lehninger principles of biochemistry (5th ed.). New York; New Delhi: W.H. Freeman.
3. Asuhiko Nozaki AND Charles Tanford “The Solubility of Amino Acids and Related Compounds in Aqueous Urea Solutions”.
4. Hopp TP. (1989) Use of hydrophilicity plotting procedures to identify protein antigenic segments and other interaction sites. Methods Enzymol., 178, 571-585.
5. Modern Applications of Plant Biotechnology in Pharmaceutical Sciences, 2015 by Saurabh Bhatia.