1 Introduction  
2 Notation and Problem Statement  
3 Model Architectures  
3.1 Sequence-based Encoder  
3.2 Structure-based Encoder  
3.3 Sequence-structure Encoder  
4 Pretext Task  
4.1 Sequence-based Pretext Task  
4.2 Structure-based Pretext Task  
4.3 Sequence-structure Pretext Task  
5 Downstream Tasks (Applications)  
5.1 Protein Property Prediction  
5.2 Protein (Complex) Structure Prediction  
5.3 Protein Design  
5.4 Structure-Based Drug Design  
6 Deep Insights and Future Outlooks  
6.1 Deeper Insights  
6.2 Future Outlooks  
7 Conclusions