Alphafold Database Fetch And Analyze
google-deepmind/science-skills
Retrieve and analyze AlphaFold predicted structures for a protein.
Structure prediction with Protenix, an open AlphaFold3 reproduction.
Install Protenix
$ npx skills add adaptyvbio/protein-design-skills --skill protenix -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install adaptyvbio/protein-design-skills protenix --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/adaptyvbio/protein-design-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/protenix .claude/skills/protenix && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "protenix" agent skill from https://github.com/adaptyvbio/protein-design-skills/tree/main/skills/protenix into .claude/skills/protenix/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protenix", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/adaptyvbio/protein-design-skills/tree/main/skills/protenixType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add adaptyvbio/protein-design-skills --skill protenix -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install adaptyvbio/protein-design-skills protenix --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/adaptyvbio/protein-design-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/protenix .agents/skills/protenix && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "protenix" agent skill from https://github.com/adaptyvbio/protein-design-skills/tree/main/skills/protenix into .agents/skills/protenix/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protenix", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add adaptyvbio/protein-design-skills --skill protenix -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install adaptyvbio/protein-design-skills protenix --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/adaptyvbio/protein-design-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/protenix .cursor/skills/protenix && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "protenix" agent skill from https://github.com/adaptyvbio/protein-design-skills/tree/main/skills/protenix into .cursor/skills/protenix/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protenix", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/adaptyvbio/protein-design-skills.git --path skills/protenix--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add adaptyvbio/protein-design-skills --skill protenix -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install adaptyvbio/protein-design-skills protenix --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/adaptyvbio/protein-design-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/protenix .gemini/skills/protenix && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "protenix" agent skill from https://github.com/adaptyvbio/protein-design-skills/tree/main/skills/protenix into .gemini/skills/protenix/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protenix", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install adaptyvbio/protein-design-skills protenixInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add adaptyvbio/protein-design-skills --skill protenix -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/adaptyvbio/protein-design-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/protenix .github/skills/protenix && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "protenix" agent skill from https://github.com/adaptyvbio/protein-design-skills/tree/main/skills/protenix into .github/skills/protenix/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protenix", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add adaptyvbio/protein-design-skills --skill protenix -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install adaptyvbio/protein-design-skills protenix --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/adaptyvbio/protein-design-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/protenix .opencode/skills/protenix && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "protenix" agent skill from https://github.com/adaptyvbio/protein-design-skills/tree/main/skills/protenix into .opencode/skills/protenix/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protenix", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
protenix- GitHub stars
- 163
- Used in
- 2 other repos
- Token cost
- ~695 tokens
- SKILL.md length
- 227 words
- Files
- 1
- Skills in repo
- 24
- Repo updated
- First seen
- Licence
- MIT
At a glance
Structure prediction with Protenix, an open AlphaFold3 reproduction.
- Predicting complex structures with an AF3-class model
- SKILL.md covers Prerequisites, How to run, Key parameters and When to use Protenix vs Boltz…, plus 1 more section
- Calls git and uv; reaches github.com
- Wanting an open alternative to AF3 alongside Boltz and Chai
What it does
Protenix is an agent skill from adaptyvbio/protein-design-skills. 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.
Its SKILL.md is about 700 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Protein structure and design. The repository describes itself as: Claude Code skills for protein design. The licence is MIT.
When your agent uses it
- Predicting complex structures with an AF3-class model
- Wanting an open alternative to AF3 alongside Boltz and Chai
- Validating designed binder-target complexes
Example prompts
- “/protenix”
What it can do on your machine
Read from SKILL.md and the folder at commit 59dd633. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
gituv
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
github.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Protenix loads about 695 tokens when it runs. Until then it costs about 84 tokens; SKILL.md has 227 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from adaptyvbio/protein-design-skills at commit 59dd633, republished under its MIT licence (© adaptyvbio). 227 words, ~695 tokens.
Download SKILL.mdSave it as
.claude/skills/protenix/SKILL.md (or your agent's skills folder).- name
- protenix
- description
- 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.
- license
- MIT
- category
- design-tools
- tags
- structure-prediction, validation, alphafold3, open-source
- biomodals_script
- modal_protenix.py
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-msaKey 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.
© adaptyvbio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/protenix of adaptyvbio/protein-design-skills.
Open the folder on GitHubat commit 59dd633
Used in 2 other repositories
We found 3 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in adaptyvbio/protein-design-skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Protenix next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Protenix this skilladaptyvbio/protein-design-skills | 163 | 2 repos | ~695 | Automated safety check: Pass | MIT | |
| Alphafold Database Fetch And Analyzegoogle-deepmind/science-skills | 3.2k | 2 repos | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Pymol VisualizationChatMol/ChatMol | 372 | — | ~1.2k | Automated safety check: Pass | MIT | |
| Complexa Binder DesignNVIDIA-BioNeMo/bionemo-agent-toolkit | 478 | — | ~3.1k | Automated safety check: Notes | Apache-2.0 | |
| DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3k | Automated safety check: Notes | MIT | |
| Biopipelineslocbp-uzh/biopipelines | 109 | — | ~2.4k | Automated safety check: Pass | MIT |
Similar skills
Pymol Visualization
ChatMol/ChatMol
Generate publication-quality molecular visualization images using PyMOL.
Complexa Binder Design
NVIDIA-BioNeMo/bionemo-agent-toolkit
Run a complete protein binder design campaign with NVIDIA Proteina-Complexa: resolve a target structure and hotspots from a name/sequence/PDB, co-design binder sequence+structure with reward-guided…
DiffDock Molecular Docking
K-Dense-AI/scientific-agent-skills
Predicts how small molecules bind to a protein with DiffDock, covering batch docking, pose ranking by confidence and checks on the results; not for binding affinity.
Biopipelines
locbp-uzh/biopipelines
Design and run computational protein and ligand workflows on a GPU: binder and enzyme design, de novo backbone generation, inverse folding and sequence redesign, structure prediction, protein-ligand…
Protein Binder Design
NVIDIA-BioNeMo/bionemo-agent-toolkit
Orchestrate an end-to-end de novo protein binder design campaign against a protein target by composing BioNeMo NIM skills.
More from adaptyvbio/protein-design-skills
All 24 skills in this repoAlphafold
adaptyvbio/protein-design-skills
Validate protein designs using AlphaFold2 structure prediction.
Bindcraft
adaptyvbio/protein-design-skills
End-to-end binder design using BindCraft hallucination. An agent skill from adaptyvbio/protein-design-skills.
Boltzgen
adaptyvbio/protein-design-skills
All-atom protein design using BoltzGen diffusion model. An agent skill from adaptyvbio/protein-design-skills.
Chai
adaptyvbio/protein-design-skills
Structure prediction using Chai-1, a foundation model for molecular structure.
Protein Design Workflow
adaptyvbio/protein-design-skills
End-to-end guidance for protein design pipelines. An agent skill from adaptyvbio/protein-design-skills.
Protein Qc
adaptyvbio/protein-design-skills
Quality control metrics and filtering thresholds for protein design.
Related
Categories
Questions about Protenix
What does Protenix do?
Structure prediction with Protenix, an open AlphaFold3 reproduction. Protenix is an agent skill from adaptyvbio/protein-design-skills. Structure prediction with Protenix, an open AlphaFold3 reproduction.
When should I use Protenix?
Protenix fits situations like: predicting complex structures with an AF3-class model; wanting an open alternative to AF3 alongside Boltz and Chai; validating designed binder-target complexes.
How do I install Protenix in Claude Code?
Run `npx skills add adaptyvbio/protein-design-skills --skill protenix -a claude-code`. Or copy the skill folder (skills/protenix in adaptyvbio/protein-design-skills) into .claude/skills/protenix in your project. Claude Code loads it when a task matches its description.
How do I install Protenix in Codex?
Run `npx skills add adaptyvbio/protein-design-skills --skill protenix -a codex`. Or copy the skill folder (skills/protenix in adaptyvbio/protein-design-skills) into .agents/skills/protenix in your project. Codex loads it when a task matches its description.
Can I use Protenix in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add adaptyvbio/protein-design-skills --skill protenix -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/protenix, .gemini/skills/protenix, .github/skills/protenix and .opencode/skills/protenix in your project.
What does Protenix need to run?
Going by SKILL.md and its folder, Protenix needs the command-line tools its instructions call (git and uv).
Does Protenix access the network?
SKILL.md names 1 domain. In commands or code: github.com; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.
Is Protenix safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Protenix use?
Protenix is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Protenix use?
About 695 tokens (SKILL.md is roughly 2.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Protenix?
Skills that share tags, products or a category with Protenix: Alphafold Database Fetch And Analyze (google-deepmind/science-skills, 3.2k stars), Pymol Visualization (ChatMol/ChatMol, 372 stars), Complexa Binder Design (NVIDIA-BioNeMo/bionemo-agent-toolkit, 478 stars) and DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Protenix?
adaptyvbio (a GitHub organization) maintains it in adaptyvbio/protein-design-skills, which has 163 GitHub stars. The repository holds 24 skills in this directory. The repository was last updated on June 11, 2026.
Source: adaptyvbio/protein-design-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.