AntiFold

1-5 minutesPaperCodeProduction Ready

Design sequences for antibodies

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_ready_api_slurm_antifold_inverse_folding
Storage: Production runtime staged: shared Python 3.10 Torch env plus 478MB AntiFold site layer and 541MB model.pt
Strategy: Production Ready using /home/nik/bio_server_venvs/binding_ddg_py310_mamba Python 3.10/Torch runtime, /media/nik/seagate_nik/bio_server/envs/antifold_py310_site dependency layer, and staged AntiFold repo/model under /media/nik/seagate_nik/bio_server/repos/antifold.
Next: Production Ready for AntiFold antibody inverse-folding on PDB inputs. Optional hardening: add UI controls for chains/regions/temperature/sample count, validate nanobody example, and package this Python 3.10 runtime as a dedicated SIF for portability.

Real dependency stack exceeded 5GB cap. 2026-07-17T01:18:00+08:00 SOP Need >5GB next-10 audit: remains Need >5GB. AntiFold has public BSD-3-Clause upstream and model weights, but current backend probe failed because /media/nik/seagate_nik/bio_server/tools/antifold/container/python310.sif does not exist. Existing local generic-smoke output is not upstream AntiFold. Needs real AntiFold runtime/model bundle and benchmark. 2026-07-18T22:34:12+08:00 SOP Need >5GB continuation batch: Official source cloned to /media/nik/seagate_nik/bio_server/repos/antifold at 789d467 (4MB). Public AntiFold model downloaded successfully to /media/nik/seagate_nik/bio_server/repos/antifold/models/model.pt (541MB). Small overlay installed fair-esm, pygam, progressbar2, and python-utils, and source import reached antifold.main. Python 3.12 overlay validation then failed on missing biotite; a follow-up no-deps pip attempt for biotite/PyG stalled before writing files and was stopped. Keep active Need >5GB because a clean Python 3.10 CUDA PyTorch/PyG SIF is required before real benchmark/adapter validation. 2026-07-19T00:58:40+08:00 SOP production validation: promoted from Need >5GB to Production Ready. Built/reused Python 3.10 AntiFold runtime with /home/nik/bio_server_venvs/binding_ddg_py310_mamba, AntiFold dependency layer /media/nik/seagate_nik/bio_server/envs/antifold_py310_site (about 478MB), official source /media/nik/seagate_nik/bio_server/repos/antifold rev 789d467, and public model /media/nik/seagate_nik/bio_server/repos/antifold/models/model.pt (541MB). Direct backend benchmark on official 6y1l_imgt.pdb passed and produced 6y1l_imgt_HL.csv 44,435 bytes and FASTA 979 bytes with AntiFold score 0.2934 and two sampled sequences. Added real cluster runner adapter and registry entry. Runner API job 1d67f95e0823 / Slurm 826 completed with artifacts summary.json, results.csv, antifold_scores.csv, antifold_sequences.fasta, antifold_log.txt, stdout/stderr, and empty slurm.err. API artifact sizes: results.csv 44,435 bytes, FASTA 979 bytes, log 1,210 bytes; sample scores 0.6507 and 0.6364, seq_recovery 0.9558.