Can anyone recommend any tool to determine the antigenicity, immunogenicity of a protein sequences?
Check the following link, hope it helps:
1) http://imed.med.ucm.es/Tools/antigenic.pl
2) http://tools.iedb.org/main/tcell/
3) http://www.epiquest.co.uk/
Check the following link, hope it helps:
1) http://imed.med.ucm.es/Tools/antigenic.pl
2) http://tools.iedb.org/main/tcell/
3) http://www.epiquest.co.uk/
Hi
check the website of the Technical university of Denmark. It is an amazing source
http://www.cbs.dtu.dk/services/
Just for Immunological features the site has the programs the list below plus programs for nucleotide and amino acid analysis:
ArrayPitope - Residue-level epitope mapping of antigens based on peptide microarray data
BepiPred - Linear B-cell epitopes
DiscoTope - Discontinuous B-cell epitopes
HLArestrictor - Patient-specific HLA restriction elements and optimal epitopes within peptides
LYRA - Lymphocyte receptor automated modelling
MHCcluster - MHC class 1 clustring based on binding specififcity
NetChop - Proteasomal cleavages (MHC ligands)
NetCTL -Integrated class I antigen presentation
NetCTLpan -Pan-specific integrated class I antigen presentation
NetMHC - Binding of peptides to MHC class I alleles
NetMHCcons- Binding of peptides to any known MHC class I molecule
NetMHCII - Binding of peptides to MHC class II alleles
NetMHCIIpan - Pan-specific binding of peptides to MHC class II alleles of known sequence
NetMHCpan - Pan-specific binding of peptides to MHC class I alleles of known sequence
NetMHCstab - Stability of peptide:MHC-I complexes
NetTepi - T-cell epitopes restricted to prevalent HLA-A and HLA-B molecules
NNAlign - Identifying sequence motifs in quantitative peptide data
PickPocket -binding of peptides to any known MHC class I molecule using binding pocket matrix extrapolation
VDJsolver - Analysis of human immunoglobulin VDJ recombination
Yes, there are several programs of Bioinformatics on line, such as, BcePred (Prediction of continuos B-cell epitope in antigenic sequences using physico-chemical propierties) (Saha et al., 2004, 2005), Kolaskar & Togaonkar antigenicity (Kolaskar and Togaonkar, 1990).
you can find different tools and their web link in the review article.
Article Novel in silico tools for designing peptide-based subunit va...
Thanks to all for this discussion and identification of websites/programs! I am reinitiating a reverse vaccinology approach in my lab to identify antigens for anti-tick vaccine development. We had intended to use a program known as Vaxijen, but it was limited to input of single sequence. Obviously, we didn't want to input 30,000 amino acids sequences one at a time, so these other alternatives give us more routes to consider for our project!
Some of them see to me specific for human and we will be looking at bovine responses to candidate antigen proteins, but still helpful!
Any other recommendations??
Felix G.
Hello, I recommend using the above algorithms and servers to generate a consensus antibody epitope prediction, then cross-reference and evaluate consensus predictions in light of relevant molecular information available for your target molecule(s). Further, 3-D structure will enhance epitope prediction and selection for further work, and structure modelling should be investigated if solved 3-D structures are not available. Good luck!
The Drug Design Group at the Medical University of Sofia hosts a number of immunogenicity and allergenicity prediction tools - AllerTOP, EpiTOP, VaxiJen to name a few; these and many more are available from the group's website:
http://www.ddg-pharmfac.net/ddg/services.html
Needless to say, explaining the methods they are based on is too long for a post on Researchgate; you should consult the relevant papers.
Hope this will be helpful to predict immunogenicity
https://www.frontiersin.org/articles/10.3389/fimmu.2018.01369/full
The tool is CD4episcore and it is freely available at IEDB.
http://tools.iedb.org/CD4episcore/
If any one is looking immunogenic protein for vaccine candidate!!!!!
http://14.139.240.55/vaccine/home.html
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-211
Yes,
BcePred (Prediction of continuos B-cell epitope in antigenic sequences) http://crdd.osdd.net/raghava/bcepred/
https://www.iedb.org/ here you have a set of different tool to apply and predict not only immunogenicity but B cell epitopes, MHC binding among others :)
Hi,
If you want to predict B-Cell epitopes, use the following program
iBCE-EL: A New Ensemble Learning Framework for Improved Linear B-Cell Epitope Prediction (http://thegleelab.org/iBCE-EL)
The above method is the latest one and developed with a larger experimentally validated dataset.
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