January 8, 2025
Journal Article
Artificial Intelligence Transforming Post-Translational Modification Research
Abstract
Post-Translational Modifications (PTMs) are covalent changes to amino acids that occur after protein synthesis, including covalent modifications on side chains and peptide backbones. Many PTMs profoundly impact cellular and molecular functions and structures, and their significance extends to evolutionary studies as well. In light of these implications, we have explored how artificial intelligence (AI) can be utilized in researching PTMs. Initially, we discuss the rationales for adopting AI and its advantages in understanding the functions of PTMs. Then, we compare various deep learning architectures and programs, including recent applications of language models, for predicting PTM sites on proteins and the regulatory functions of these PTMs. Finally, we describe our high-throughput PTM data generation pipeline, which formats data suitably for AI training and predictions. Therefore, we hope this review illuminates areas where future AI models on PTMs can be improved, thereby contributing to the field of PTM bioengineering.Published: January 8, 2025