Protein structure prediction in the deep learning era

Significant advances have been achieved in protein structure prediction, especially with the recent development of the AlphaFold2 and the RoseTTAFold systems. This article reviews the progress in deep learning-based protein structure prediction methods in the past two years. First, we divide the representative methods into two categories: the two-step approach and the end-to-end approach. Then, we show that the two-step approach is possible to achieve similar accuracy to the state-of-the-art end-to-end approach AlphaFold2. Compared to the end-to-end approach, the two-step approach requires fewer computing resources. We conclude that it is valuable to keep developing both approaches. Finally, a few outstanding challenges in function-orientated protein structure prediction are pointed out for future development.