I am looking for an epitope prediction program that would take into account the hydrophobicity of the amino acid residues within the peptide sequences to predict T-cell (class I & II) epitopes. The only one i could find was from an article published by Chowell et al. (2015) -> (https://www.ncbi.nlm.nih.gov/pubmed/25831525). The problem however is that their prediction program was developed in-house, so they have not made it available for others to use.
Hi Romel,
Our lab has previously used IEDB database for epitope prediction.
But, i don't think there is any parameter for incorporating hydrophobicity of amino acids within a peptide sequence.
IEDB is freeware and is quite accurate in its prediction capability.
regards
Tanuj
You may check the following link:
http://iclab.life.nctu.edu.tw/POPI/
The help page says they take into account a number of physicochemical properties which includes hydrophobicity.
You may also check their paper in Bioinformatics:
https://doi.org/10.1093/bioinformatics/btm061
Thank you so very much for your input, Tanuj Sharma, and Debasree Sarkar, for finding exactly what I was looking for.
You may use NetCTL also to predict T-cell (class I & II) epitopes
http://www.cbs.dtu.dk/services/NetCTL/
Usam Mirza, the website for NetCTL states that it can only predict for MHC class I. I might need to look into it more closely to see if that is true. Anyway, Thank you for your suggestion.
Mario,
You can read this work as I used a number of tools for such predictions. This might help you.
Regards,
Article Towards peptide vaccines against Zika virus: Immunoinformati...
You might consider adapting the methods in this paper, which could even be implemented in MS Excel. "Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: A critical role for the muscarinic receptor type 3 " https://www.researchgate.net/publication/299336974_Common_molecular_mechanism_of_the_hepatic_lesion_and_the_cardiac_parasympathetic_regulation_in_chronic_hepatitis_C_infection_A_critical_role_for_the_muscarinic_receptor_type_3
Article Common molecular mechanism of the hepatic lesion and the car...
Thanks you Dr. Mirza and Mr. Cavanaugh for your suggestions. I will look into them as soon as I am able to.
Hi Dr Soyza. Please let us know if you have any questions. Regards. David
Will do, Mr. David.
And I am not a Dr. yet, still doing my Masters, haha
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics