title: Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction.
abstract: BACKGROUND
  The immunogenicity of peptides depends on their ability to bind to MHC molecules. MHC binding affinity prediction methods can save significant amounts of experimental work. The class II MHC binding site is open at both ends, making epitope prediction difficult because of the multiple binding ability of long peptides.
  
  
  RESULTS
  An iterative self-consistent partial least squares (PLS)-based additive method was applied to a set of 66 peptides no longer than 16 amino acids, binding to DRB1*0401. A regression equation containing the quantitative contributions of the amino acids at each of the nine positions was generated. Its predictability was tested using two external test sets which gave r(pred) = 0.593 and r(pred) = 0.655, respectively. Furthermore, it was benchmarked using 25 known T-cell epitopes restricted by DRB1*0401 and we compared our results with four other online predictive methods. The additive method showed the best result finding 24 of the 25 T-cell epitopes.
  
  
  BACKGROUND
  Peptides used in the study are available from http://www.jenner.ac.uk/JenPep. The PLS method is available commercially in the SYBYL molecular modelling software package. The final model for affinity prediction of peptides binding to DRB1*0401 molecule is available at http://www.jenner.ac.uk/MHCPred. Models developed for DRB1*0101 and DRB1*0701 also are available in MHCPred.
authors: Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK.
authors: I A
authors: IA
authors: Doytchinova
authors: D R
authors: DR
authors: Flower
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D020650:Combinatorial Chemistry Techniques; D003198:Computer Simulation; D018984:Epitopes, T-Lymphocyte / Q000032:analysis / Q000737:chemistry* / Q000145:classification* / Q000276:immunology; D000949:Histocompatibility Antigens Class II / Q000032:analysis / Q000737:chemistry* / Q000145:classification* / Q000276:immunology; D007118:Immunoassay / Q000379:methods; D016018:Least-Squares Analysis; D008958:Models, Molecular; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013329:Structure-Activity Relationship
chemical_list: D018984:Epitopes, T-Lymphocyte; D000949:Histocompatibility Antigens Class II