StaB-ddG

1-5 minutesPaperCodeProduction Ready

Predict mutational effects on protein-protein binding from folding energy

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_pass_stabddg_cpu_map_location
Storage: <5
Strategy: shared python312_slim.sif + stabddg_py312_site + sequence_design_torch_cpu_py312/palm layers with CPU map_location wrapper
Next: Production Ready. Optional hardening: support uploaded PDB mutation batches without source-tree output collision.

No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 SOP batch recheck: backend inventory found no staged StaB-ddG source/runtime/artifacts/runner. Upstream uses Python 3.10/Torch with bundled model_ckpts and example PDB/mutation command; suitable for a small shared PyTorch smoke after staging. Kept Smoke Pending. 2026-07-05 18:35 +08:00 backend re-audit: no StaB-ddG backend artifacts, Slurm result, or API runner evidence found; small Python 3.10/Torch smoke remains pending. Kept Smoke Pending. 2026-07-06 implementation pass: cloned LDeng0205/StaB-ddG at /media/nik/seagate_nik/bio_server/tools/stab-ddg/source/StaB-ddG rev b19a5d72637a6b581b16f38af39383658e5ae1a5. Repo includes model_ckpts/proteinmpnn.pt, stabddg.pt, stability_finetuned.pt and examples/one_mutation/1AO7.pdb. Direct Slurm job 459 passed at /media/nik/seagate_nik/bio_server/runs/stab-ddg/smoke_20260706_162500 using shared python312_slim.sif plus sequence_design_torch_cpu_py312/palm_py312_site. The smoke ran the official one_mutation example EA63Q,QD30V,KA66A on 1AO7 chains ABC_DE with mc_samples=2, using a tiny CPU wrapper only to add map_location=cpu for CUDA-saved checkpoint loading. It produced output.csv/results.csv with finite pred_1=1.3839722, summary.json, copied 1AO7_output artifacts, stdout/stderr, job.log, slurm.out, and empty slurm.err. 2026-07-08T20:47:39+08:00: Production Ready promotion: backend runner API job a15a8d4c0cbe / Slurm job 564 completed cleanly using shared python312_slim.sif, stabddg/sequence_design_torch_cpu/palm layers, bundled 1AO7 example, and CPU map_location wrapper for CUDA-saved checkpoint. Produced zero-byte slurm.out/slurm.err, one-row output.csv/results.csv, and finite pred_1 1.3839111 for EA63Q,QD30V,KA66A.