… All MHC-peptide pairs in the dataset have an IC 50 score between 1 nM and 50,000 nM. …
the same supertype displaying higher functional similarity, while the MHC molecules in different …

… In order to combine information of position-specific amino acid scores of the nonapeptides
with AAPPs, we define a score S k,i (n) for the i th amino acid of the nonapeptide n under a k …

… MHC We next proceeded to investigate whether the peptides bound in various MHC–peptide …
their binding energy scores from all possible overlapping peptides of similar length present …

… limited MHC sequence similarity to human MHC molecules, … prediction methods for peptide
binding to MHC molecules, is … the pairwise BLOSUM50 similarity scores between the amino …

… extract the appropriate parameters for the binding score calculations. The advantage of the
… groove, and because we showed that the different structural templates give very similar …

… in a peptide score that reflects its binding energy. Here we present our analysis for peptide
binding to four MHC … solved peptides bind to the MHC molecules in a very similar fashion, …

… similarity score that is calculated between pHLAs. The input is a list of peptides and the
structures of those peptides … We calculate the sequence similarity between peptides as well as …

… The first is to obtain a large set of structures and use the structure with the most similar
peptide for the peptides that do not have an experimentally determined structure. The other …

… Additive method: This method consists of a scoring matrix + pair coefficients, similar to our
SMM + pair coefficients approach. It has been recently introduced by (Doytchinova et al., 2002)…

… Vice versa held true for the amino-terminus with a similar yet weaker perturbation observed
… score. The same held true for randomization of isoleucine at position 2, underlining a similar …