Rankpep: prediction of binding peptides to Class I and Class II MHC molecules
Description
This server predicts peptide binders to MHCI and MHCII molecules from protein sequence/s or sequence alignments using Position Specific Scoring Matrices (PSSMs). In addition, it predicts those MHCI ligands whose C-terminal end is likely to be the result of proteasomal cleavage. A detailed explanation of the method can be found here.
PSSM
SELECT PSSM (Check MHCI or MHCII)
MHC I MHC II
OR, UPLOAD YOUR PSSM
INPUT
TYPE: FASTA sequence/s CLUSTALW multiple sequence alignment
Replace example with your query
OR, UPLOAD SEQUENCES
BINDING THRESHOLD
PERCENTAGE: TOP NUMBER:
PROTEASOME
CLEAVAGE
FILTER: LMPC :
If Filter is ON only peptides predicted to be cleaved are shown
IMMUNODOMINANCE
FILTER: THRESHOLD :
If Filter is ON only peptides to be immmunodominant will be selected
ADVANCED OPTONS
RESTRICT RESULTS BY MW
Lower Limit for Molecular Weight
Upper Limit for Molecular Weight
VARIABILITY MASKING

Select Variability Threshold
Value must range between 0.0 and 4.3


Citation:
  • Reche PA, Glutting JP and Reinherz EL Prediction of MHC Class I Binding Peptides Using Profile Motifs. Human Immunology 63, 701-709 (2002).
  • Reche PA, Glutting JP, Zhang H, Reinherz EL.Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. 456:405-419 (2004)
  • Manoj Bhasin, Ellis L. Reinhez and Pedro A. Reche. Modeling features of immunodominance into T-cell epitope identification. 2nd International Immunoinformatics Symposium, Boston University, March 7-9, 2005.
Questions, and suggestions to: Pedro Reche
Hits since June/2002 Last updated: March/2004
MIF Bioinformatics Molecular Immunology Foundation