Foundation models of protein sequences: A brief overview

Protein sequence models have evolved from simple statistics of aligned families to versatile foundation models of evolutionary scale. Enabled by self-supervised learning and an abundance of protein sequence data, such foundation models now play a central role in protein science. They facilitate rich representations, powerful generative design, and fine-tuning across diverse domains. In this review, we trace modeling developments and categorize them into methodological trends over the modalities they describe and the contexts they condition upon. Following a brief historical overview, we focus our attention on the most recent trends and outline future perspectives.