An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions
Abstract
:1. Introduction
2. Methods
2.1. Data Preparation
2.2. Construction of Physical-Feature Collection in LLPhyScore
3. Results and Discussion
3.1. Predictor Training
3.2. Model Performance Comparison against Different Negative Training Sets
3.3. Predictor Validation
3.4. Comparison of Prediction Using Eight Features or Single Features
3.5. Comparison between LLPhyScore and Other Phase-Separation Predictors
3.6. Feature-Based Breakdown of Scores for Different Sequences
3.7. Gene Ontology Term Enrichment
3.8. Physical Insights into Phase Separation Based on LLPhyScores of the PDB Set
3.9. High-Scoring Structures in the PDB Trend towards Disorder
4. Conclusions
5. Technical Methods
5.1. Curation of PS-Positive Sequences
5.2. Clustering of PS-Positive Sequences
5.3. Preparation of PS-Negative Sequences
5.4. Construction of Training/Test/Evaluation Datasets
5.5. Physical-Feature-Based Sequence Representation
5.6. Predictor Training
5.7. Proteome Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Cai, H.; Vernon, R.M.; Forman-Kay, J.D. An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions. Biomolecules 2022, 12, 1131. https://doi.org/10.3390/biom12081131
Cai H, Vernon RM, Forman-Kay JD. An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions. Biomolecules. 2022; 12(8):1131. https://doi.org/10.3390/biom12081131
Chicago/Turabian StyleCai, Hao, Robert M. Vernon, and Julie D. Forman-Kay. 2022. "An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions" Biomolecules 12, no. 8: 1131. https://doi.org/10.3390/biom12081131
APA StyleCai, H., Vernon, R. M., & Forman-Kay, J. D. (2022). An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions. Biomolecules, 12(8), 1131. https://doi.org/10.3390/biom12081131