Protenix Agent Skill

> Structure prediction with Protenix, an open AlphaFold3 reproduction. Use this (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.

694 tokens

context cost

the whole folder, loaded on every use

files

instructions only

copies elsewhere

how many repositories repackaged it

151

stars on the repo

on the repository, not the skill itself

Install

one command, takes just this skill from the repository

npx skills add https://github.com/adaptyvbio/protein-design-skills --skill protenix

The instruction itself

6 sections, as written by the author

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.

Other skills for the same job

different authors, same section of the catalogue

Protocolsio Integration

by christophacham

×4

Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.

16k tokens

Tailored Resume Generator

by frostant

×4

Analyzes job descriptions and generates tailored resumes that highlight relevant experience, skills, and achievements to maximize interview chances

3k tokens

Excalidraw Diagram Generator

by github

vendor ×3

Generate Excalidraw diagrams from natural language descriptions. Use when asked to "create a diagram", "make a flowchart", "visualize a process", "draw a system architecture", "create a mind map", or "generate an Excalidraw file". Supports flowcharts, relationship diagrams, mind maps, and system architecture diagrams. Outputs .excalidraw JSON files that can be opened directly in Excalidraw.

Build and distribute Expo development clients locally or via TestFlight

Use when you have a written implementation plan to execute in a separate session with review checkpoints

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

16k tokens

Benchling Integration

by christophacham

×3

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

24k tokens

How to use it

Copy the folder

Take adaptyvbio/protenix from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.