Molecular descriptor subset selection in theoretical peptide quantitative structure-retention relationship model development using nature-inspired optimization algorithms.
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 out of 102 peptides originating from Bacillus subtilis proteomes (RMSEP of 22.030%). Its applicability domain was defined, from which it was evident that the developed GA-QSRR exhibited strong robustness. All the sources of the model's error were identified, thus allowing for further application of the developed methodology in proteomics.
Department of Chemical Engineering, Pukyong National University , 365 Sinseon-ro, 608-739 Busan, Korea.
Petar
P
Žuvela
Department of Chemical Engineering, Pukyong National University , 365 Sinseon-ro, 608-739 Busan, Korea.
J Jay
JJ
Liu
Laboratory of Mass Spectrometry, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk , Kładki 24, 80-822 Gdańsk, Poland.
Katarzyna
K
Macur
Department of Pharmaceutical Chemistry, Medical University of Gdańsk , Hallera 107, 80-416 Gdańsk, Poland.
Tomasz
T
Bączek
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001185:Artificial Intelligence; D001412:Bacillus subtilis / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D003198:Computer Simulation; D006801:Humans; D016018:Least-Squares Analysis; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D001426:Bacterial Proteins; D010455:Peptides; D011506:Proteins