Agent-driven protein engineering platform
Web UI · REST API · CLI · 40+ models · 11+ databases
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VenusFactory2 puts protein language models, biological databases, and an Agent orchestrator in one place: upload a sequence/structure to predict, drive multi-step analysis in natural language, or fine-tune your own models.
Try online: venusfactory.bio
| Prerequisite | Notes |
|---|---|
| Python | ≥3.12 (installer creates a 3.12 .venv by default) |
| Node.js | 25.x + npm (WebUI v2 build) |
| Disk | Reserve several–15+ GB (PyTorch wheels dominate) |
| GPU | Optional; NVIDIA → CUDA wheels, else CPU |
Slow Hugging Face access: export HF_ENDPOINT=https://hf-mirror.com
git clone --recurse-submodules https://github.com/AI4Protein/VenusFactory2.git && cd VenusFactory2
# If you already cloned without submodules:
# git submodule update --init --recursive
python scripts/setup_quickstart.py # interactive one-click install
# python scripts/setup_quickstart.py -y # CI / non-interactive
source .venv/bin/activate
python src/webui_v2.py --host 0.0.0.0 --port 7861
# → http://localhost:7861The installer detects older setups (.venv / frontend / weights) and can reuse or wipe them. Press Enter for the recommended path.
After launch
- Open the UI → Quick Tools work without an LLM key
- Agent: set an API key in Settings, or
cp .env.example .env(see.env.example) - Optional check:
python scripts/check_env.py
Three layers — start at the top; dig only when needed:
| Layer | Where |
|---|---|
| Map of all docs | docs/README.md |
| Install · catalogs · WebUI map · CLI/API | docs/wiki/Home.md |
| Per-feature how-tos | docs/manual/ |
| Agent skills (authors) | src/agent/skills/AGENTS.md · docs/agent/SKILLS_INDEX.md · docs/agent/CONTRIBUTING_SKILLS.md |
中文：README_CN.md · docs/README.md
@article{tan2026venusfactory2,
title={Self-evolving AI agents for protein discovery and directed evolution},
author={Tan, Yang and Zhang, Lingrong and Li, Mingchen and Yu, Yuanxi and Zhong, Bozitao and Zhou, Bingxin and Dong, Nanqing and Hong, Liang},
journal={arXiv preprint arXiv:2603.27303},
year={2026}
}
@inproceedings{tan2025venusfactory,
title={VenusFactory: An Integrated System for Protein Engineering with Data Retrieval and Language Model Fine-Tuning},
author={Tan, Yang and Liu, Chen and Gao, Jingyuan and Banghao, Wu and Li, Mingchen and Wang, Ruilin and Zhang, Lingrong and Yu, Huiqun and Fan, Guisheng and Hong, Liang and others},
booktitle={Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations)},
pages={230--241},
year={2025}
}Released under the VenusFactory Non-Commercial License: free for academic / non-commercial use; commercial use needs written approval → hongl3lilang@sjtu.edu.cn. See LICENSE / LICENSE_CN.md.
Maintained by Liang's Lab, Shanghai Jiao Tong University.
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