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. 2002 Jun;28(2):183–194. doi: 10.1023/A:1019931731519

Prediction of MHC Class I Binding Peptides by a Query Learning Algorithm Based on Hidden Markov Models

Keiko Udaka 1,✉, Hiroshi Mamitsuka 2, Yukinobu Nakaseko 1, Naoki Abe 2
PMCID: PMC3456669  PMID: 23345768

Abstract

A query learning algorithm based on hidden Markov models (HMMs) isdeveloped to design experiments for string analysis and prediction of MHCclass I binding peptides. Query learning is introduced to aim at reducingthe number of peptide binding data for training of HMMs. A multiple numberof HMMs, which will collectively serve as a committee, are trained withbinding data and used for prediction in real-number values. The universeof peptides is randomly sampled and subjected to judgement by the HMMs.Peptides whose prediction is least consistent among committee HMMs aretested by experiment. By iterating the feedback cycle of computationalanalysis and experiment the most wanted information is effectivelyextracted. After 7 rounds of active learning with 181 peptides in all,predictive performance of the algorithm surpassed the so far bestperforming matrix based prediction. Moreover, by combining the bothmethods binder peptides (log Kd < -6) could be predicted with84% accuracy. Parameter distribution of the HMMs that can be inspectedvisually after training further offers a glimpse of dynamic specificity ofthe MHC molecules.

Keywords: algorithm, binding, experimental design, MHC class I molecules, peptides, prediction, query learning, specificity, string analysis

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