Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores
J Salomon, DR Flower - BMC bioinformatics, 2006 - Springer
… similarity scores between pairs of peptides. For each pair, a similarity score is composed of
multiple sub-scores … influence that each sub-score will have on the cumulative score. In turn, it …
multiple sub-scores … influence that each sub-score will have on the cumulative score. In turn, it …
Prediction of peptide-MHC binding using profiles
PA Reche, EL Reinherz - Immunoinformatics: predicting immunogenicity in …, 2007 - Springer
… by its similarity to a set of known peptide–MHC binders … peptide can be considered a binder
if it has a score within the range of scores of the peptides known to bind to the relevant MHC …
if it has a score within the range of scores of the peptides known to bind to the relevant MHC …
On evaluating MHC-II binding peptide prediction methods
… for assigning weights to similar peptides as opposed to eliminating similar peptides from
the … The LA kernel measures the similarity between two sequences by adding up the scores …
the … The LA kernel measures the similarity between two sequences by adding up the scores …
Methods for prediction of peptide binding to MHC molecules: a comparative study
… scoring reflects the frequency of the respective amino acid in natural MHC ligands, T-cell
epitopes, or binding peptides … Our results do, however, suggest that HMMs provide similar …
epitopes, or binding peptides … Our results do, however, suggest that HMMs provide similar …
Prediction of MHC class I binding peptides using profile motifs
PA Reche, JP Glutting, EL Reinherz - Human immunology, 2002 - Elsevier
… peptide sequence (query) to a given MHC molecule is linked to its similarity to a group of
aligned peptides … identify potential binders, we score all the peptide sequences included in the …
aligned peptides … identify potential binders, we score all the peptide sequences included in the …
Properties of MHC class I presented peptides that enhance immunogenicity
JJA Calis, M Maybeno, JA Greenbaum… - PLoS computational …, 2013 - journals.plos.org
… Similar to our result based on murine data (Figure 4A), the human epitopes had a much
higher score in the immunogenicity model than the non-epitopes (Wilcoxon rank-sum test: p = …
higher score in the immunogenicity model than the non-epitopes (Wilcoxon rank-sum test: p = …
Prediction of MHC class I binding peptides, using SVMHC
P Dönnes, A Elofsson - BMC bioinformatics, 2002 - Springer
… scores can be calculated from observed amino-acid frequencies in each position or be set
manually. The sum of the scores for a given peptide … From the similar behavior of these three …
manually. The sum of the scores for a given peptide … From the similar behavior of these three …
A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach
… Others base similar scoring matrices on multiple peptide … similar to our previous effort
for MHC class I molecules [38]. We present a large dataset of unpublished MHC class II-peptide …
for MHC class I molecules [38]. We present a large dataset of unpublished MHC class II-peptide …
MHC-NP: predicting peptides naturally processed by the MHC
… a broad estimate of their similarity. However, for most proteins, notably for MHC, peptide–protein …
For this reason, we propose to use the F1 score to evaluate our method's discriminative …
For this reason, we propose to use the F1 score to evaluate our method's discriminative …
Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior
… Our results indicate that, at least for peptide:MHC class I binding predictions, scoring
matrices can provide competitive prediction performances. This close prediction performances …
matrices can provide competitive prediction performances. This close prediction performances …
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