Protenix

Skill adaptyvbio/protein-design-skills/skills/protenix

Claude Code skills for protein design

Install

npx -y skills add adaptyvbio/protein-design-skills --skill protenix

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What its author says it does

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Structure prediction with Protenix, an open AlphaFold3 reproduction. Use this skill when: (1) Predicting complex structures with an AF3-class model, (2) Wanting an open alternative to AF3 alongside Boltz and Chai, (3) Validating designed binder-target complexes. For QC thresholds, use protein-qc. For ipSAE ranking, use ipsae.

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SKILL.md

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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

Requirement	Value
Runner	Modal (biomodals)
GPU	L40S (default; `GPU` env var)
Setup	See Getting started

How to run

git clone https://github.com/hgbrian/biomodals && cd biomodals

printf '>protein|A\nMAWTPLLLLLLSHCTGSLSQ...\n' > target.faa

uv run --with modal modal run modal_protenix.py \
  --input-faa target.faa \
  --seeds 42 \
  --no-use-msa

Key parameters

Parameter	Default	Description
`--input-faa`	one required	FASTA input (or `--input-json`)
`--seeds`	`42`	Comma-separated seeds
`--use-msa` / `--no-use-msa`	MSA on	Pass `--no-use-msa` for single-sequence
`--model-name`	v1 base	Set `protenix-v2` for antibody-antigen complexes
`--use-mini`	off	Switch to the smaller `protenix_mini` model
`--out-dir`	`./out/protenix`	Output directory

When to use Protenix vs Boltz vs Chai

Need	Tool
Affinity head (small molecules)	boltz (Boltz-2)
Fastest, ligand support	chai
Open AF3 reproduction	protenix (v1 base)
Antibody-antigen complexes	protenix-v2

Ranking a shortlist across more than one predictor is more reliable than trusting a single model.

Troubleshooting

Issue	Cause	Fix
Missing input error	No `--input-faa`/`--input-json`	Provide one
Slow run	MSA enabled	Add `--no-use-msa`
OOM	Large complex	Use `--use-mini` or a larger GPU

Next: Rank with ipsae, filter with protein-qc.