openfold3

openfold3 is a skill for Claude Code, Codex from UnicomAI/wanwu. It costs 60 tokens per session (2,150 once invoked), scanned A, a copy of openfold3, Apache-2.0.

A protein-structure prediction tool based on OpenFold3, an open-source reproduction of AlphaFold3. It predicts the shapes of complexes containing proteins, nucleic acids, and small molecules.

In plain words
What is it for?
Use it to predict the three-dimensional structure of a protein, DNA or RNA, and ligand complex from suitable input data.
Why use it?
It lets developers run this type of structure prediction with open model weights, provided the required Python, CUDA, memory, storage, and model access are available.

Skill for Claude CodeCodex

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/unicomai/wanwu/openfold3
Any agent
npx skills add UnicomAI/wanwu --skill openfold3
Clone the repo
git clone --depth 1 https://github.com/UnicomAI/wanwu

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for openfold3

README.md
[![agentmods](https://agentmods.dev/badge/skills/unicomai/wanwu/openfold3.svg)](https://agentmods.dev/skills/unicomai/wanwu/openfold3)
Your own site
<a href="https://agentmods.dev/skills/unicomai/wanwu/openfold3"><img src="https://agentmods.dev/badge/skills/unicomai/wanwu/openfold3.svg" alt="Measured on agentmods" height="20"></a>
Per session 60 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,150 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin 100% copy Near-identical to another mod in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00060 $0.02150
Opus 5 $0.00030 $0.01075
Sonnet 5 $0.00012 $0.00430
Haiku 4.5 $0.00006 $0.00215

Measured 4d ago against content hash eef2b03a2c7e, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

openfold3 scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

This is a copy

100% identical to openfold3 — 73 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

configs/microservice/bff-service/configs/agent-skills/claude-science/openfold3/SKILL.md · 185 lines

How it starts

The opening of the file, as written. The whole thing — 185 lines — stays where its author put it; the contents beside it link to each section on GitHub.

OpenFold3 Structure Prediction

Prerequisites

Requirement Minimum Recommended
Python 3.10+ 3.11
CUDA 12.1+ 12.4+
GPU VRAM 24GB 80GB (H100)
RAM 32GB 64GB
Disk (weights) 3GB -

How to run

Installation

pip install 'openfold3[cuequivariance]==0.4.1'

The default attention kernel is DeepSpeed DS4Sci_EvoformerAttention. If DeepSpeed is unavailable, switch to the cuEquivariance triangle kernels (no build-from-source) by overriding the eval memory settings in model_config.py (use_deepspeed_evo_attention: False, use_cueq_triangle_kernels: True). Some pre-built environments already ship this override; check before re-patching.

Weights

Apache-2.0, ~2.3 GB from HF OpenFold/OpenFold3. The repo is gated (auto-approval) — accept the access form on the HF model page and authenticate (huggingface-cli login or HF_TOKEN) before downloading:

export OPENFOLD_CACHE=~/.openfold3
huggingface-cli download OpenFold/OpenFold3 checkpoints/of3-p2-155k.pt \
  --local-dir "$OPENFOLD_CACHE"

run_openfold will also auto-download to $OPENFOLD_CACHE on first run if egress is open and HF credentials are available (either HF_TOKEN or a prior huggingface-cli login) with repo access granted. The interactive setup_openfold helper exists but prompts on stdin; prefer the explicit download above for non-interactive runs.

Running

export OPENFOLD_CACHE=/path/to/cache
run_openfold predict \
  --query_json=queries.json \
  --output-dir out/ \
  --use-msa-server false \
  --use-templates false

run_openfold discovers the checkpoint under $OPENFOLD_CACHE automatically. Only pass --inference-ckpt-path <file.pt> if you have a non-standard layout or multiple checkpoints and need to pin one explicitly.

For MSA + templates (slower, higher accuracy), drop the two false flags. The MSA server is api.colabfold.com; template chain-ID remap hits data.rcsb.org (GraphQL) — both must be reachable.

Read the full file on GitHub · 185 lines

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 4d ago First seen · 185 lines · 60 tokens per session scan A eef2b03a2c7e

Subscribe to this mod's changes

openfold3 is a skill published in the GitHub repository UnicomAI/wanwu (2,455 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 60 tokens to every session and 2,150 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. It is 100% identical to openfold3, differing in 73 lines, and is treated as a copy.

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