The binding affinities of the peptides to the selected class II MHC type are calculated using the Regularized Thermodynamic Average, or RTA, method.  The prediction of peptides binding to class II MHC is complicated by the fact that, unlike for class I MHC, the peptide can bind in multiple registers due to a MHC binding cleft that is open at both ends allowing the peptide termini to extend beyond the MHC.  The RTA method accounts for the contribution of all of these possible peptide binding registers through a thermodynamic average.  It also reduces overfitting through a regularization penalty.  Details of the RTA method are described in Bordner and Mittleman, "Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model", BMC Bioinformatics 2009.

Each peptide sequence should be contained in a separate line.  The sequences can either be pasted into the window above or can be uploaded as a separate file.

Please send any questions or comments to RTA@bordnerlab.org.