EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks
Abstract
:1. Introduction
2. Results and Discussion
3. Materials and Methods
3.1. Datasets
3.2. Training Procedure
3.3. Model Architectures
3.4. Implementation
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
Multimer | Multiple Chain Protein |
Monomer | Single Chain Protein |
EMA | Model Accuracy Estimation |
CASP | The Critical Assessment of Protein Structure Prediction |
GNN | Graph Neural Network |
FCL | Fully Connected Layer |
EBM | Energy-Based Model |
CB | Beta Carbon |
CA | Alpha Carbon |
CDP | Contact Dependent Potential |
RSAP | Relative Solvent Accessibility Potential |
MSE | Mean Squared Error |
L1 | Mean Absolute Error |
TM-score | Overall Fold Score |
QS-score | Overall Interface Score |
DCG | Discounted Cumulative Gain |
NDCG | Normalized Discounted Cumulative Gain |
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Type | Backbone | TM-L1 | TM-MSE | QS-L1 | QS-MSE |
---|---|---|---|---|---|
Regression | Transformer | 0.243 | 0.094 | 0.314 | 0.127 |
EBM | Transformer | 0.245 | 0.096 | 0.341 | 0.156 |
Regression | MetaLayer | 0.263 | 0.098 | 0.300 | 0.124 |
EBM | MetaLayer | 0.242 | 0.088 | 0.299 | 0.126 |
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Siciliano, A.J.; Zhao, C.; Liu, T.; Wang, Z. EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks. Int. J. Mol. Sci. 2024, 25, 6250. https://doi.org/10.3390/ijms25116250
Siciliano AJ, Zhao C, Liu T, Wang Z. EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks. International Journal of Molecular Sciences. 2024; 25(11):6250. https://doi.org/10.3390/ijms25116250
Chicago/Turabian StyleSiciliano, Andrew Jordan, Chenguang Zhao, Tong Liu, and Zheng Wang. 2024. "EGG: Accuracy Estimation of Individual Multimeric Protein Models Using Deep Energy-Based Models and Graph Neural Networks" International Journal of Molecular Sciences 25, no. 11: 6250. https://doi.org/10.3390/ijms25116250