Progress in protein pre-training models integrating structural knowledge

Abstract

The AI revolution, sparked by natural language and image processing, has brought new ideas and research paradigms to the field of protein computing. One significant advancement is the development of pre-training protein language models through self-supervised learning from massive protein sequences. These pre-trained models encode various information about protein sequences, evolution, structures, and even functions, which can be easily transferred to various downstream tasks and demonstrate robust generalization capabilities. Recently, researchers have further developed multimodal pre-trained models that integrate more diverse types of data. The recent studies in this direction are summarized and reviewed from the following aspects in this paper. Firstly, the protein pre-training models that integrate protein structures into language models are reviewed: this is particularly important, for protein structure is the primary determinant of its function. Secondly, the pre-trained models that integrate protein dynamic information are introduced. These models may benefit downstream tasks such as protein-protein interactions, soft docking of ligands, and interactions involving allosteric proteins and intrinsic disordered proteins. Thirdly, the pre-trained models that integrate knowledge such as gene ontology are described. Fourthly, we briefly introduce pre-trained models in RNA fields. Finally, we introduce the most recent developments in protein designs and discuss the relationship of these models with the aforementioned pre-trained models that integrate protein structure information.