Peptide Synthesis Design and Tools

How to predict Antigenic peptides?
There are certain rules that can be used to predict antigenicity. Using these, there will be a greater chance of the antibody recognizing the native protein.

  • Antigenic peptides is advised to be located in solvent accessible region and contain both the hydrophobic and hydrophilic residues

Softwares like DSSP, NACESS and WHATIF can be use to determine solvent accessibility of known 3D structure of proteins. If 3D structures are not known, programmes like PHD, JPRED and ACCpro will help.

  • Choose peptides in long loops connecting Secondary Structures motif, avoid helical regions, to increase the chance of recognition by the antibody.
  • Pick the N and C terminals, these are solvent accessible.

Other suitable online tools include:

ExPASy, tools for protein identification, characterization and DNA sequence analysis 

A list of molecular databases from NCBI including; Nucleotide Databases, Protein Databases, Structure Databases, Taxonomy Databases, Genome Databases and Expression Databases.