S-Pred: protein structural property prediction using MSA transformer

Abstract

Predicting the local structural features of a protein from its amino acid sequence helps its function prediction to be revealed and assists in three-dimensional structural modeling. As the sequence-structure gap increases, prediction methods have been developed to bridge this gap. Additionally, as the size of the structural database and computing power increase, the performance of these methods have also significantly improved. Herein, we present a powerful new tool called S-Pred, which can predict eight-state secondary structures (558), accessible surface areas (ASAs), and intrinsically disordered regions (IDRs) from a given sequence. For feature prediction, S-Pred uses multiple sequence alignment (MSA) of a query sequence as an input. The MSA input is converted to features by the MSA Transformer, which is a protein language model that uses an attention mechanism. A long short-term memory (LSTM) was employed to produce the final prediction. The performance of S-Pred was evaluated on several test sets, and the program consistently provided accurate predictions. The accuracy of the 558 prediction was approximately 76%, and the Pearson's correlation between the experimental and predicted ASAs was 0.84. Additionally, an IDR could be accurately predicted with an F1-score of 0.514. The program is freely available at https://github.com/arontier/S_Pred_Paper and https://ad3.io as a code and a web server.