Dayhoff is an Atlas of both protein sequence data and generative language models — a centralized resource that brings together 3.34 billion protein sequences across 1.7 billion clusters of metagenomic and natural protein sequences (GigaRef), 46 million structure-derived synthetic sequences (BackboneRef), and 16 million multiple sequence alignments (OpenProteinSet). These models can natively predict zero-shot mutation effects on fitness, scaffold structural motifs by conditioning on evolutionary or structural context, and perform guided generation of novel proteins within specified families. Learning from metagenomic and structure-based synthetic data from the Dayhoff Atlas increased the cellular expression rates of generated proteins, highlighting the real-world value of expanding the scale, diversity, and novelty of protein sequence data