Journal
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
Volume 45, Issue 1, Pages 236-243Publisher
ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER
DOI: 10.1016/j.ejmech.2009.09.049
Keywords
Proteochemometrics; QSAR; Epitope prediction; MHC class II
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Funding
- National Science Fund of Ministry of Education and Science, Bulgaria [02-115/2008]
- Senior Jenner Fellowship
- Wellcome Trust [WT079287MA]
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A proteochemometrics approach was applied to a set of 2666 peptides binding to 12 HLA-DRB1 proteins. Sequences of both peptide and protein were described using three z-descriptors. Cross terms accounting for adjacent positions and for every second position in the peptides were included in the models, as well as cross terms for peptide/protein interactions. Models were derived based on combinations of different blocks of variables. These models had moderate goodness of fit, as expressed by r(2), which ranged from 0.685 to 0.732: and good cross-validated predictive ability, as expressed by q(2), which varied from 0.678 to 0.719. The external predictive ability was tested using a set of 356 HLA-DRB1 binders, which showed an r(pred)(2) in the range 0.364-0.530. Peptide and protein positions involved in the interactions were analyzed in terms of hydrophobicity, steric bulk and polarity. (C) 2009 Elsevier Masson SAS. All rights reserved.
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