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In this study, we proposed a stacking framework-based approach called FRTpred that predicts protein logarithmic folding rate constant ln(kf) and folding type from the provided sequence. Firstly, 30 base-models (regression models for folding rate and classification models for folding type) were constructed by integrating 10 representative feature extraction methods and three commonly used machine-learning algorithms. Subsequently, the predicted values of 30 base-models were combined and inputted to random forest algorithm and constructed the final prediction model. Cross-validation analysis showed that FRTpred achieved mean absolute deviation of 1.491, 2.016, and 1.954 for non-two-state (N2S), two-state (2S), and combined (2S+N2S) ln(kf) prediction. Moreover, it predicts folding type with an accuracy of 0.843. Performance comparisons based on independent test against the existing methods showed that FRTpred is more precise and promising in both ln(kf) and folding type prediction. |
FRTpred: A stacking framework-based prediction of protein folding rate and its types from the sequence (Submitted).
[Please cite this paper if you find FRTpred useful in your research]