T charge as a descriptor shows a clear bias. The charge can indefinitely increase or decrease with the sequence, while the other descriptors have a maximum and a minimum value. For this reason, in this study the Title Loaded From File average net charge at physiological pH was utilized. However, the use of averaged descriptors causes a second bias, since shuffled sequences will have the same averaged values [20,43]. In our previous work the hydrophobic moment was proposed to solve this bias [20]. Nevertheless, the PCA shows that hydrophobic moment may not be a good property for the antimicrobial activity prediction of cysteine-stabilized peptides. Therefore, the properties must be carefully used together with the cysteine patterns of cysteine-stabilized AMPs. We state that this predictor must be used for cysteine stabilized peptides with a known pattern or a previously identified domain, since those descriptors are going to be only significant if the sequence is in its correct order. In fact, the descriptors selection through PCA was useful for developing a more accurate antimicrobial activity prediction system, since the three kernel functions reach higher accuracies in the k-fold cross validation in comparison to our previous work [20]. While in this work the kernels reach accuracies of at least 84.19 (linear and radial kernels), in our previous work, the bestTable 4. Title Loaded From File Benchmarking of prediction methods using the BS1 and BS2.Model CS-AMPPred Linear CS-AMPPred Polynomial CS-AMPPred Radial ANFIS CAMP SVM CAMP Discriminant Analysis CAMP Random Forest SVM doi:10.1371/journal.pone.0051444.tSensitivity 81.25 87.50 88.28 96.88 91.41 95.31 92.97 89.Specificity 90.62 87.50 87.50 85.94 85.94 82.03 35.94 43.Accuracy 85.94 87.50 87.89 91.41 88.67 88.67 64.45 66.PPV 89.65 87.50 87.60 87.32 86.67 84.14 59.20 61.MCC 0.72 0.75 0.76 0.83 0.77 0.78 0.35 0.Reference This work This work This work [25] [23] [23] 1531364 [23] [20]CS-AMPPred: The Cysteine-Stabilized AMPs Predictoraccuracy on k-fold cross validation was 77 (polynomial kernel) [20]. Here, the best accuracy was also reached by the polynomial kernel, with 85.81 . This accuracy improvement indicates that the five selected descriptors (average hydrophobicity, average charge, flexibility, and indexes of a-helix and loop formation) showed higher efficiency than the four descriptors previously described by Porto et al. [20] (net charge at physiological pH, average hydrophobicity, hydrophobic moment and amphipathicity). The receiver-operating characteristic (ROC) curves obtained for each kernel function against the blind data set (Figure 3) show that the models are underestimated in 5-fold cross validation, which also was observed in our previous work [20]. The accuracy of each model increases by ,5 against the blind data set; the highest accuracies are obtained with the polynomial and radial kernels (90 ), while the linear kernel shows 89.33 of accuracy. Furthermore, the MCC indicate that the tree models have a good quality prediction, with values of 0.79, 0.80 and 0.80 for linear, radial and polynomial kernels, respectively. In addition, the models have a PPV of 89.33 , 86.59 and 86.59 , respectively. Although the model based on the polynomial kernel was the best one for overall prediction concerning the blind data set and 5fold cross validation, the models based on linear and radial kernels were better predictors than the polynomial kernel for some individual classes, such as b-defensins, CSab defensins, cyclotides and pept.T charge as a descriptor shows a clear bias. The charge can indefinitely increase or decrease with the sequence, while the other descriptors have a maximum and a minimum value. For this reason, in this study the average net charge at physiological pH was utilized. However, the use of averaged descriptors causes a second bias, since shuffled sequences will have the same averaged values [20,43]. In our previous work the hydrophobic moment was proposed to solve this bias [20]. Nevertheless, the PCA shows that hydrophobic moment may not be a good property for the antimicrobial activity prediction of cysteine-stabilized peptides. Therefore, the properties must be carefully used together with the cysteine patterns of cysteine-stabilized AMPs. We state that this predictor must be used for cysteine stabilized peptides with a known pattern or a previously identified domain, since those descriptors are going to be only significant if the sequence is in its correct order. In fact, the descriptors selection through PCA was useful for developing a more accurate antimicrobial activity prediction system, since the three kernel functions reach higher accuracies in the k-fold cross validation in comparison to our previous work [20]. While in this work the kernels reach accuracies of at least 84.19 (linear and radial kernels), in our previous work, the bestTable 4. Benchmarking of prediction methods using the BS1 and BS2.Model CS-AMPPred Linear CS-AMPPred Polynomial CS-AMPPred Radial ANFIS CAMP SVM CAMP Discriminant Analysis CAMP Random Forest SVM doi:10.1371/journal.pone.0051444.tSensitivity 81.25 87.50 88.28 96.88 91.41 95.31 92.97 89.Specificity 90.62 87.50 87.50 85.94 85.94 82.03 35.94 43.Accuracy 85.94 87.50 87.89 91.41 88.67 88.67 64.45 66.PPV 89.65 87.50 87.60 87.32 86.67 84.14 59.20 61.MCC 0.72 0.75 0.76 0.83 0.77 0.78 0.35 0.Reference This work This work This work [25] [23] [23] 1531364 [23] [20]CS-AMPPred: The Cysteine-Stabilized AMPs Predictoraccuracy on k-fold cross validation was 77 (polynomial kernel) [20]. Here, the best accuracy was also reached by the polynomial kernel, with 85.81 . This accuracy improvement indicates that the five selected descriptors (average hydrophobicity, average charge, flexibility, and indexes of a-helix and loop formation) showed higher efficiency than the four descriptors previously described by Porto et al. [20] (net charge at physiological pH, average hydrophobicity, hydrophobic moment and amphipathicity). The receiver-operating characteristic (ROC) curves obtained for each kernel function against the blind data set (Figure 3) show that the models are underestimated in 5-fold cross validation, which also was observed in our previous work [20]. The accuracy of each model increases by ,5 against the blind data set; the highest accuracies are obtained with the polynomial and radial kernels (90 ), while the linear kernel shows 89.33 of accuracy. Furthermore, the MCC indicate that the tree models have a good quality prediction, with values of 0.79, 0.80 and 0.80 for linear, radial and polynomial kernels, respectively. In addition, the models have a PPV of 89.33 , 86.59 and 86.59 , respectively. Although the model based on the polynomial kernel was the best one for overall prediction concerning the blind data set and 5fold cross validation, the models based on linear and radial kernels were better predictors than the polynomial kernel for some individual classes, such as b-defensins, CSab defensins, cyclotides and pept.
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