iAmyP: A Multi-view Learning for Amyloidogenic Hexapeptides Identification Based on Sequence Least Squares Programming

Abstract

The development of peptide drug is hindered by the risk of amyloidogenic aggregation; if peptides tend to aggregate in this manner, they may be unsuitable for drug design. Computational methods aimed at predicting amyloidogenic sequences often face challenges in extracting high-quality features, and their predictive performance can be enchanced. To surmount these challenges, iAmyP was introduced as a specialized computational tool designed for predicting amyloidogenic hexapeptides. Utilizing multi-view learning, iAmyP incorporated sequence, structural, and evolutionary features, performing feature selection and feature fusion through recursive feature elimination and attention mechanisms. This amalgamation of features and subsequent feature selection and fusion lead to optimal performance facilitated by an optimization algorithm based on sequence least squares programming. Notably, iAmyP exhibited robust generalization for peptides with lengths of 7-10 amino acids. The role of hydrophobic amino acids in the aggregation process is critical, and a thorough analysis have significantly enhanced our insight into their significance in amyloidogenic hexapeptides. This tool represented an advancement in the development of peptide therapeutics by providing an understanding of amyloidogenic aggregation, establishing itself as a valuable framework for assessing amyloidogenic sequences. The data and code can be freely accessed at https://github.com/xialab-ahu/iAmyP .

Keywords: Amyloidogenic hexapeptide; Feature fusion; Multi-view learning; Sequential least squares.