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README.md

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+---
+license: apache-2.0
+library_name: transformers
+pipeline_tag: other
+---
+
+# Proteo-R1: Reasoning Foundation Models for De Novo Protein Design
+
+This repository contains the **generate** checkpoint of Proteo-R1, a reasoning-guided protein design framework that decouples molecular understanding from geometric generation. It uses a dual-expert architecture where a multimodal large language model (Qwen3 + Protenix) serves as the understanding expert, and a diffusion-based generation expert (Boltz1) performs conditional co-design under hard constraints.
+
+- Paper: [Proteo-R1: Reasoning Foundation Models for De Novo Protein Design](https://huggingface.co/papers/2605.02937)
+- Project page: [https://smiles724.github.io/r1/](https://smiles724.github.io/r1/)
+- Code: [https://github.com/smiles724/Proteo-R1](https://github.com/smiles724/Proteo-R1)
+
+## Quickstart
+
+The model is used via two command-line tools: `proteor1-prepare-cdr` and `proteor1-design`. Both checkpoints are pulled automatically from the Hugging Face Hub.
+
+```bash
+# Step 1: emit per-CDR hidden states
+proteor1-prepare-cdr \
+  --cif data/demo/8q7o_A__C/8q7o_A__C.cif \
+  --design-points "$(cat data/demo/8q7o_A__C/design_points.txt)" \
+  --out work/smoke/prepare_cdr \
+  --record-id 8q7o_A__C \
+  --emit-cdr-hidden \
+  --understand-ckpt thinking-bio-lab/proteor1-understand \
+  --override
+
+# Step 2: structure design with framework inpainting
+proteor1-design \
+  --input_dir data/demo_canonical_yamls/8q7o_A__C.yaml \
+  --output work/smoke \
+  --checkpoint thinking-bio-lab/proteor1-generate \
+  --precomputed_cdr_dir work/smoke/prepare_cdr/8q7o_A__C/cdr_hidden \
+  --processed_msa_dir data/demo_msa \
+  --structure_inpainting \
+  --ground_truth_structure_dir data/demo_gt_structures \
+  --no_cdr_json \
+  --override
+```
+
+See the [GitHub README](https://github.com/smiles724/Proteo-R1) for full installation instructions, troubleshooting, and additional examples.
+
+## Citation
+
+```bibtex
+@article{wu2026proteo,
+  title={Proteo-R1: Reasoning Foundation Models for De Novo Protein Design},
+  author={Wu, Fang and Xuan, Weihao and Qi, Heli and Cao, Hanqun and Chang, Heng-Jui and Zhou, Zeqi and Zhao, Haokai and Jian, Ma and Ma, Carl and Cheng, Yu-Chi and others},
+  journal={arXiv preprint arXiv:2605.02937},
+  year={2026}
+}
+```