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QSPR-perturbation models for the prediction of B-epitopes from immune epitope database: an interesting route for predicting “in silico” new optimal peptide sequences and/or boundary conditions for vaccine development.
Severo Vázquez-Prieto
* 1 ,
Esperanza Paniagua
2 ,
Florencio M. Ubeira
2
1  Laboratorio de Biología Celular y Molecular, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET, Facultad de Ciencias Veterinarias, UNCPBA, Tandil, Argentina.
2  Laboratorio de Parasitología, Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Santiago de Compostela, Campus Vida, Santiago de Compostela 15782, Spain
Published: 02 December 2015 by MDPI in MOL2NET'15, Conference on Molecular, Biomed., Comput. & Network Science and Engineering, 1st ed. congress NICEXSM-01: North-Ibero-American Congress on Exp. and Simul. Methods, Valencia-Miami, USA, 2015
https://doi.org/10.3390/MOL2NET-1-b007
Abstract:

In the present study, three different physicochemical molecular properties for peptides were calculated using the program MARCH-INSIDE: atomic polarizability, partition coefficient, and polarity. These measures were used as input parameters of a Linear Discriminant Analysis (LDA) in order to develop three different quantitative structure-property relationship (QSPR)-perturbation models for the prediction of B-epitopes reported in the immune epitope database (IEDB) given perturbations in peptide sequence, in vivo process, experimental techniques, and source or host organisms. The accuracy, sensitivity and specificity of the models were >90% for both training and cross-validation series. The statistical parameters of the models were compared to the results achieved with the electronegativity QSPR-perturbation model previously reported. The results indicate that this type of approach may constitute an interesting route for predicting “in silico” new optimal peptide sequences and/or boundary conditions for vaccine development.

Keywords: Epitopes; Vaccine design; Perturbation theory; QSAR/QSPR models; Markov Chains
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Comments on this paper
Andrey Toropov
10 December 2015
Whether mentioned databases are available for internet users?
This is very interesting work. Whether mentioned databases are available for internet users?
Severo Vázquez Prieto
11 December 2015
Dear Andrey Toropov, thank you so much for your comment. Our database was constructed from information obtained from www.iedb.org and, for the moment, is not available for internet users.



 
 
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