Molecular descriptor subset selection in theoretical peptide quantitative structure-retention relationship model development using nature-inspired optimization algorithms

Analytical Chemistry
Petar ŽuvelaTomasz Bączek

Abstract

In this work, performance of five nature-inspired optimization algorithms, genetic algorithm (GA), particle swarm optimization (PSO), artificial bee colony (ABC), firefly algorithm (FA), and flower pollination algorithm (FPA), was compared in molecular descriptor selection for development of quantitative structure-retention relationship (QSRR) models for 83 peptides that originate from eight model proteins. The matrix with 423 descriptors was used as input, and QSRR models based on selected descriptors were built using partial least squares (PLS), whereas root mean square error of prediction (RMSEP) was used as a fitness function for their selection. Three performance criteria, prediction accuracy, computational cost, and the number of selected descriptors, were used to evaluate the developed QSRR models. The results show that all five variable selection methods outperform interval PLS (iPLS), sparse PLS (sPLS), and the full PLS model, whereas GA is superior because of its lowest computational cost and higher accuracy (RMSEP of 5.534%) with a smaller number of variables (nine descriptors). The GA-QSRR model was validated initially through Y-randomization. In addition, it was successfully validated with an external testing set o...Continue Reading

References

Feb 21, 2004·Bioinformatics·Robertson Craig, Ronald C Beavis
Oct 12, 2004·Journal of Proteome Research·Lewis Y GeerStephen H Bryant
Apr 15, 2006·Science·Bruno Domon, Ruedi Aebersold
Aug 28, 2007·Bioinformatics·Yvan SaeysPedro Larrañaga
Sep 21, 2007·Journal of Chemical Information and Modeling·Christoph RückerMarkus Meringer
Jan 25, 2008·Proteomics·Kosaku ShinodaYasushi Ishihama
Mar 11, 2008·Journal of Molecular Graphics & Modelling·Shane Weaver, M Paul Gleeson
Oct 22, 2008·Journal of Pharmaceutical and Biomedical Analysis·K BodziochY Vander Heyden
Feb 19, 2009·Journal of Chromatographic Science·Jahanbakhsh Ghasemi, Saadi Saaidpour
Mar 14, 2009·Electrophoresis·Martin GilarJohn C Gebler
Jun 12, 2009·Human Molecular Genetics·Aurélie DipietromariaReiner A Veitia
Jan 29, 2010·Journal of the Royal Statistical Society. Series B, Statistical Methodology·Hyonho Chun, Sündüz Keleş
May 6, 2010·Analytica Chimica Acta·Zou XiaoboMao Hanpin
May 6, 2010·Talanta·K BodziochY Vander Heyden
Nov 1, 1996·Analytical Chemistry·V CentnerC Sterna
Jul 19, 2011·Chromatographia·S StudzińskaB Buszewski
Feb 22, 2012·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Mohammad GoodarziYvan Vander Heyden
Jun 4, 2013·Journal of Chromatography. a·Angelo Antonio D'ArchivioMaria Anna Maggi
Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates
Jan 9, 2014·The Onderstepoort Journal of Veterinary Research·Davies M Pfukenyi, Samson Mukaratirwa
Mar 13, 2014·European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences·Vladimir DobričićOlivera Čudina
Dec 3, 2014·Analytica Chimica Acta·Mohammad Goodarzi, Leandro dos Santos Coelho
Feb 24, 2015·Journal of Pharmaceutical and Biomedical Analysis·Renata BujakMichał J Markuszewski

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Citations

Feb 6, 2018·Journal of Computational Chemistry·Petar ŽuvelaMing Wah Wong
Mar 10, 2017·Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes·Kobra ZareiMonire Ahmadi
Jul 29, 2017·Analytical and Bioanalytical Chemistry·Cecilia RossettiLéon Reubsaet
Nov 30, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Krzesimir CiuraJarosław Sączewski
Jul 10, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Petar ŽuvelaTomasz Bączek
May 25, 2021·Journal of the American Society for Mass Spectrometry·Reza AalizadehNikolaos S Thomaidis
Feb 13, 2019·Journal of Chemical Information and Modeling·T M WhiteheadG J Conduit

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