A deep attention network for predicting amino acid signals in the formation of α-helices

The secondary and tertiary structure of a protein has a primary role in determining its function. Even though many folding prediction algorithms have been developed in the past decades — mainly based on the assumption that folding instructions are encoded within the protein sequence — experimental techniques remain the most reliable to establish protein structures. In this paper, we searched for signals related to the formation of α-helices. We carried out a statistical analysis on a large dataset of experimentally characterized secondary structure elements to find over- or under-occurrences of specific amino acids defining the boundaries of helical moieties. To validate our hypothesis, we trained various Machine Learning models, each equipped with an attention mechanism, to predict the occurrence of α-helices. The attention mechanism allows to interpret the model’s decision, weighing the importance the predictor gives to each part of the input. The experimental results show that different models focus on the same subsequences, which can be seen as codes driving the secondary structure formation.