Research map / Probabilistic and scientific modeling / Molecules and proteins
Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem
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Measured effects reported in the paper
| What was changed | Where | Measured | Effect |
|---|---|---|---|
| Use SMCDiff particle filtering instead of fixed motif inpainting | ProtDiff motif scaffolding · 5trv | lower-quartile motif RMSD | Helped |
| Use SMCDiff particle filtering instead of replacement inpainting | ProtDiff motif scaffolding · 5trv | lower-quartile motif RMSD | Helped |
| Use SMCDiff rather than fixed or replacement inpainting | ProtDiff motif scaffolding · Out-of-distribution RSV and EF-hand motifs | median motif RMSD | Helped |
| Increase scaffold length | SMCDiff + ProtDiff · 5trv | motif RMSD | Mixed |
| Generate unconditional backbones with ProtDiff | ProtDiff · Unconditional sampling, lengths 50–128 | designable samples (scTM > 0.5): 11.8%; short 17%; long 9% | Mixed |
| Use a reflection-equivariant model that does not encode chirality | ProtDiff · Unconditional backbone samples | samples with incorrect left-handed helices: 45% | Hurt |
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