title: EpiTOP--a proteochemometric tool for MHC class II binding prediction.
abstract: BACKGROUND
  T-cell epitope identification is a critical immunoinformatic problem within vaccine design. To be an epitope, a peptide must bind an MHC protein.
  
  
  RESULTS
  Here, we present EpiTOP, the first server predicting MHC class II binding based on proteochemometrics, a QSAR approach for ligands binding to several related proteins. EpiTOP uses a quantitative matrix to predict binding to 12 HLA-DRB1 alleles. It identifies 89% of known epitopes within the top 20% of predicted binders, reducing laboratory labour, materials and time by 80%. EpiTOP is easy to use, gives comprehensive quantitative predictions and will be expanded and updated with new quantitative matrices over time.
  
  
  BACKGROUND
  EpiTOP is freely accessible at http://www.pharmfac.net/EpiTOP.
authors.affiliation: Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria.
authors.forename: Ivan
authors.initials: I
authors.lastname: Dimitrov
authors.forename: Panayot
authors.initials: P
authors.lastname: Garnev
authors.forename: Darren R
authors.initials: DR
authors.lastname: Flower
authors.forename: Irini
authors.initials: I
authors.lastname: Doytchinova
mesh_terms: D000483:Alleles; D018984:Epitopes, T-Lymphocyte / Q000378:metabolism*; D006684:HLA-DR Antigens / Q000378:metabolism; D059811:HLA-DRB1 Chains; D000949:Histocompatibility Antigens Class II / Q000235:genetics / Q000378:metabolism*; D008024:Ligands; D010455:Peptides / Q000276:immunology / Q000378:metabolism; D012984:Software
chemical_list: D018984:Epitopes, T-Lymphocyte; D006684:HLA-DR Antigens; D059811:HLA-DRB1 Chains; D000949:Histocompatibility Antigens Class II; D008024:Ligands; D010455:Peptides