TruMPET: A New Method for Protein Secondary Structure Prediction Using Neural Networks Trained on Multiple Pre-Selected Physicochemical and Structural Features

Protein structure prediction continues to pose multiple challenges, despite the progress made by ML. While recent deep learning models have achieved a strong performance using embeddings from protein language models, they often ignore non-canonical amino acids and rely heavily on sequence alignments or evolutionary profiles. Here, we present an improvement to this approach for predicting the secondary protein structure of DSSP classes solely from amino acid sequences. We suggest that ML feature sets should be generated from statistically significant mutually uncorrelated descriptors. The selection of statistically assessed descriptors, including predicting the physicochemical parameters of non-canonical amino acids, is a key component of the proposed method. The statistical significance and influence of each of the suggested features were assessed using a two-step Linear Discriminant Analysis, which permitted the evaluation of the statistical significance of each descriptor and their impact on model accuracy. We applied the set of 109 most influential statistically significant descriptors as a learning model for the two-layer Bi-LSTM network combined with ESMFold2 embeddings. Our method, TruMPET (Training upon Multiple Pre-selected Elements Technique), outperformed all other methods reported in the literature for the non-redundant datasets (CB513: DSSP Q3 = 91.36% and Q8 = 85.41%, TEST2018: DSSP Q3 = 90.64% and Q8 = 84.17%).