SourceStructure Language Models for Protein Conformation Generation
The paper examines the effect of sampling temperature on ESM3's zero-shot conformation generation for BPTI (n=100). At low temperatures (t=0.25), ESM3's validity drops substantially compared to t=1.0, indicating the pre-trained model produces more clash-free structures at higher temperatures. After fine-tuning (ESMdiff), this degradation is resolved. The paper notes that ESM3 and ESMdiff maintain high validity as temperature increases beyond 1.0, with minimal diversity improvement, suggesting limited sensitivity to high temperatures.