Protenix Structure Prediction

Protenix is ByteDance's open PyTorch reproduction of AlphaFold3 (Apache 2.0). It is an AF3-class complex predictor, useful next to boltz and chai for cross-checking designed complexes. Runnable through biomodals.

Use Protenix-v2 for antibody-antigen complexes. The v2 model (464M params, April 2026) adds 9 to 13 percentage points of antibody-antigen accuracy over v1 at the DockQ > 0.23 threshold and is more sample-efficient (v2 at 5 seeds exceeds v1 at 1000). Select it with --model-name protenix-v2. For general complexes, the v1 base model is fine.

Prerequisites