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Structure Language Models for Protein Conformation Generation
2025-01-22
· ICLR 2025 Poster ·
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Findings
IC-225
ESM3 (1.4B) performs zero-shot protein conformation generation with competitive quality across BPTI dynamics, conformation changing pairs, and intrinsically disordered proteins
IC-226
ESM3 (pre-trained, without fine-tuning) shows significantly degraded conformation generation validity at low sampling temperatures (t < 0.5)
IC-227
MSA-based conformation generation methods (AlphaFlow, MSA-subsampling) outperform sequence-based methods (EigenFold, STR2STR, ESMFlow) on conformation changing pair generation
IC-228
ESM3 (1.4B) fails to capture MD ensemble statistics on the ATLAS benchmark, achieving pairwise RMSD correlation of only 0.08