Stochastic-based descriptors studying peptides biological properties: modeling the bitter tasting threshold of dipeptides

Bioorganic & Medicinal Chemistry
Ronal Ramos de ArmasEugenio Uriarte

Abstract

MARCH-INSIDE methodology was applied to the prediction of the bitter tasting threshold of 48 dipeptides by means of pattern recognition techniques, in this case linear discriminant analysis (LDA), and regression methods. The LDA models yielded a percentage of good classification higher than 80% with the two main families of descriptor generated by this methodology (95.8% for self return probability and 83.3% using electronic delocalization entropy). The regression models can explain more than 80% of the experimental variance of the independent variable. Two regression models were obtained with R(2) values of 0.82 and 0.88 for the whole data and the data without two outliers, respectively; having a standard deviation of 0.27 and 0.23. The predictive power of the obtained equations was assessed by the Leave-One-Out cross validation procedures, giving the same percentages of good classification as in the training set, in the LDA models, and yielding values of q(2) of 0.78 and 0.86 in the regression model, respectively. The validation of this methodology was also carried out by comparison with previous reports modeling this data with other well-known methodologies, even 3-D molecular descriptors.

References

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Citations

Sep 17, 2008·Applied Microbiology and Biotechnology·Makoto Yagasaki, Shin-ichi Hashimoto
Jun 14, 2005·European Journal of Medicinal Chemistry·Maykel Cruz-Monteagudo, Humberto González-Díaz
Aug 6, 2005·FEBS Letters·Humberto González-DíazEugenio Uriarte
Sep 29, 2009·Analytica Chimica Acta·Francisco J Prado-PradoHumberto González-Díaz
Nov 11, 2008·Journal of Theoretical Biology·Alcides Perez-BelloHumberto González-Díaz
Apr 10, 2008·Journal of Theoretical Biology·Jianbo TongZhiliang Li
Nov 14, 2007·Journal of Computational Chemistry·Humberto González-Díaz, Francisco J Prado-Prado
Feb 26, 2008·Proteomics·Humberto González-DíazEugenio Uriarte
Jul 27, 2007·Journal of Peptide Science : an Official Publication of the European Peptide Society·Feifei TianZhiliang Li
Feb 7, 2007·Journal of Computational Chemistry·Humberto González-DíazGianni Podda
Apr 22, 2011·Journal of Computational Chemistry·Raghuvir R S PissurlenkarEvans C Coutinho
Sep 20, 2005·Bioorganic & Medicinal Chemistry Letters·Humberto González-Díaz, Eugenio Uriarte
Dec 29, 2013·BioMed Research International·Somaieh SoltaniAbolghasem Jouyban
Apr 7, 2015·Journal of Theoretical Biology·Yovani Marrero-PonceYsaías J Alvarado
Jan 27, 2005·Bioorganic & Medicinal Chemistry·Humberto González-DíazEugenio Uriarte
Dec 16, 2004·Bioorganic & Medicinal Chemistry·Humberto González-DíazRonal Ramos de Armas
Jul 26, 2006·Bulletin of Mathematical Biology·Maykel Cruz-MonteagudoYenny González-Díaz
Nov 23, 2006·Journal of Peptide Science : an Official Publication of the European Peptide Society·Jianping Wu, Rotimi E Aluko
Feb 3, 2007·Journal of Computational Chemistry·Humberto González-DíazAngeles Sánchez-González
Dec 28, 2019·Biomolecules·Guillermin Agüero-ChapinAgostinho Antunes
Mar 9, 2018·Analytical and Bioanalytical Chemistry·Dominic AgyeiChibuike C Udenigwe
Apr 1, 2020·ACS Omega·Mehri Mahmoodi-ReihaniVahid Zare-Shahabadi
Nov 9, 2005·Bioorganic & Medicinal Chemistry Letters·Humberto González-DíazYenny González-Díaz

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