Rankpep: Prediction of peptide binding to MHC molecules using profiles. Pedro A Reche

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