Protenix-v2

5-30 minutesPaperCodeNeeds Token/License

Predict protein/nucleic acid/small molecule complexes. Outperforms AlphaFold3 with major gains on antibody-antigen interfaces.

Job Name

EXAMPLES

Input Format *Protein Sequence *Protein SequencesRNA SequencesDNA sequences Add ligands to your complexLigands (CCD or SMILES)Number of samplesNumber of batchesModel

SeedNumber of Trunk Recycles Use Templates Training-Free Guidance (TFG)Pocket restraint binder chainPocket restraint pocket chainPocket contactsContact restraintsCovalent restraintsRestraints Minimum Distance (A)Restraints Maximum Distance (A)

All sequences must be non empty.

Readiness

Readiness: Needs Token/License
Smoke: passed
Artifacts: passed
Production: needs_token_license_protenix_v2_checkpoint_access_required
Storage: 5-20GB runtime/checkpoint once access is resolved
Strategy: Shared Protenix runtime plus model cache; may require Docker-derived SIF for kalign/hmmer.
Next: Resolve official protenix-v2 checkpoint access/download, then install protenix plus kalign/hmmer runtime, run tiny inference with model protenix-v2, and wire the Slurm/API adapter.

large model weights, structure DBs, docking/MD assets, or GPU stack likely >5GB 2026-07-16T20:35:00+08:00 SOP Need >5GB next-10 audit: remains Need >5GB. Registry maps to protenix-v2-smoke using toy complex_structure_smoke; no Protenix-v2 SIF/model cache/backend mapping found for real inference. 2026-07-18T18:39:16+08:00 SOP Need >5GB active batch: Read-only audit confirmed Protenix code/model license is Apache-2.0, but official v2 checkpoint access has reported 403/CDN access issues and no raw local v2 checkpoint is staged. 2026-07-18T19:02:14+08:00 SOP Need >5GB active install batch: No install completed in this continuation; remains blocked on resolving official protenix-v2 checkpoint access before tiny inference validation. 2026-07-18T20:49:48+08:00 SOP targeted make-ready/reclassify batch: Reclassified from Need >5GB to Needs Token/License because the official Protenix-v2 checkpoint access/download remains unresolved and no raw v2 checkpoint is staged. Runtime installation should wait until model access is confirmed.