Dear Razieh Veisi,

You may want to review the data presented below:

Identifying the epitope to which an antibody binds is central for many immunological applications such as drug design and vaccine development. The Pepitope server is a web-based tool that aims at predicting discontinuous epitopes based on a set of peptides that were affinity-selected against a monoclonal antibody of interest. The server implements three different algorithms for epitope mapping: PepSurf, Mapitope, and a combination of the two. The rationale behind these algorithms is that the set of peptides mimics the genuine epitope in terms of physicochemical properties and spatial organization. When the three-dimensional (3D) structure of the antigen is known, the information in these peptides can be used to computationally infer the corresponding epitope. A user-friendly web interface and a graphical tool that allows viewing the predicted epitopes were developed. Pepitope can also be applied for inferring other types of protein-protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure.

Availability: http://pepitope.tau.ac.il/

https://pubmed.ncbi.nlm.nih.gov/17977889/

Hi Razieh Veisi,

There are so many free online tools are available to predict an immunogenic peptide. The properties like antigenicity, immunogenicity, allergenicity etc has to be studied before getting into a conclusion or defining a suitable candidate.

Computational tools such as BIMAS-HLA, CTLpred, NetCTL, Propred-I, Propred-II, NetMHCpan, NetMHCstabpan, and Immune Epitope Database Analysis (IEDB) can be used according to your need.

If you wish to use one single website for prediction of peptides in almost all possible angles, use IEDB (IEDB Analysis Resource) . You will get some idea to define your workflow. Read some good reverse vaccinology related reviews or some papers to choose.

all the best

Kalyanaraman

Thanks for your answer.

Unfortunately due to unknown reasons, IEDB does not work in my laptop and I receive some errors on the results page.