Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model.

ABSTRACT:

Background

The binding of peptide fragments of extracellular peptides to class II MHC is a crucial event in the adaptive immune response. Each MHC allotype generally binds a distinct subset of peptides and the enormous number of possible peptide epitopes prevents their complete experimental characterization. Computational methods can utilize the limited experimental data to predict the binding affinities of peptides to class II MHC.

Results

We have developed the Regularized Thermodynamic Average, or RTA, method for predicting the affinities of peptides binding to class II MHC. RTA accounts for all possible peptide binding conformations using a thermodynamic average and includes a parameter constraint for regularization to improve accuracy on novel data. RTA was shown to achi

SUBMITTER: Bordner AJ 

PROVIDER: S-EPMC2828437 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature