Modeling Structure–Activity Relationship of AMPK Activation
Abstract
:1. Introduction
2. Results
2.1. Similarity of Groups
2.2. Statistical Comparison of Datasets
2.3. Random Forest Classification (RFC)
2.4. Support Vector Machine Classification (SVM-C)
2.5. Stochastic Gradient Boosting (SGB) Analysis
2.6. Logistic Regression Classification (LRC)
2.7. Deep Neural Network (DNN) Analysis
2.8. Test Performance
3. Discussion
4. Materials and Methods
4.1. Data
- “AMPK AND activation”
- “AMPK AND inhibition”
4.2. Data Preprocessing
- with their names, smiles codes, PubChem IDs, and PubMed IDs (Compounds.csv); and
- with all calculated PaDel descriptors (Data.csv) in https://github.com/cptbern/QSAR_AMPK, accessed on 27 October 2021.
4.3. Validation
4.4. Similarity
4.5. Machine Learning Models
4.6. Random Forest Classification (RFC)
4.7. Stochastic Gradient Boosting Classification (SGB)
4.8. Support Vector Machine Classification (SVM-C)
4.9. Logistic Regression Classification (LRC)
4.10. Deep Learning Neural Network (DNN)
4.11. Model Evaluation
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Sample Availability
References
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Method | Training Accuracy (%) | Test Accuracy (%) | Y-Randomization ** (%) | Test Precision (%) | Sensitivity (%) | Specificity (%) | AUC * |
---|---|---|---|---|---|---|---|
RFC | 91.6 | 92.6 | 52.7 ± 2.3 | 90.3 | 91.2 | 94.0 | 0.968 ± 0.013 |
SVM-C | 91.0 | 93.0 | 53.2 ± 2.2 | 90.1 | 93.5 | 92.4 | 0.962 ± 0.009 |
SGB | 91.3 | 93.0 | 52.8 ± 2.2 | 90.7 | 92.0 | 94.0 | 0.968 ± 0.012 |
LRC | 90.8 | 91.0 | 52.6 ± 2.1 | 89.2 | 97.4 | 94.8 | 0.948 ± 0.014 |
DNN | 91.6 | 90.6 | 53.0 ± 1.8 | 87.6 | 90.2 | 91.1 | 0.970 ± 0.002 |
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Drewe, J.; Küsters, E.; Hammann, F.; Kreuter, M.; Boss, P.; Schöning, V. Modeling Structure–Activity Relationship of AMPK Activation. Molecules 2021, 26, 6508. https://doi.org/10.3390/molecules26216508
Drewe J, Küsters E, Hammann F, Kreuter M, Boss P, Schöning V. Modeling Structure–Activity Relationship of AMPK Activation. Molecules. 2021; 26(21):6508. https://doi.org/10.3390/molecules26216508
Chicago/Turabian StyleDrewe, Jürgen, Ernst Küsters, Felix Hammann, Matthias Kreuter, Philipp Boss, and Verena Schöning. 2021. "Modeling Structure–Activity Relationship of AMPK Activation" Molecules 26, no. 21: 6508. https://doi.org/10.3390/molecules26216508
APA StyleDrewe, J., Küsters, E., Hammann, F., Kreuter, M., Boss, P., & Schöning, V. (2021). Modeling Structure–Activity Relationship of AMPK Activation. Molecules, 26(21), 6508. https://doi.org/10.3390/molecules26216508