| Abstract
| - Amino acid descriptors are often used in quantitative structure−activity relationship (QSAR)analysis of proteins and peptides. In the present study, descriptors were used to characterizepeptides binding to the human MHC allele HLA-A*0201. Two sets of amino acid descriptorswere chosen: 93 descriptors taken from the amino acid descriptor database AAindex and thez descriptors defined by Wold and Sandberg. Variable selection techniques (SIMCA, geneticalgorithm, and GOLPE) were applied to remove redundant descriptors. Our results indicatethat QSAR models generated using five z descriptors had the highest predictivity and explainedvariance (q2 between 0.6 and 0.7 and r2 between 0.6 and 0.9). Further to the QSAR analysis,15 peptides were synthesized and tested using a T2 stabilization assay. All peptides bound toHLA-A*0201 well, and four peptides were identified as high-affinity binders.
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