Create README.md

README.md

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+---
+license: mit
+library_name: fairseq
+datasets:
+  - charlesnovak/InstructPro2Bench
+tags:
+  - biology
+  - protein-design
+  - ligand-binding
+  - antibody-design
+  - pytorch
+---
+
+# InstructPro2
+
+Model weights for **[InstructPro2: Natural Language and Biological Grounding Guided De Novo Protein Design](https://arxiv.org/abs/2610.19592)** — a 3.2B protein design model that generates sequences from natural-language function descriptions, optionally conditioned on a ligand or an antigen.
+
+Code: [chovak/InstructPro2](https://github.com/chovak/InstructPro2) ·
+Data: [charlesnovak/InstructPro2Bench](https://huggingface.co/datasets/charlesnovak/InstructPro2Bench) ·
+Paper: [arXiv:2610.19592](https://arxiv.org/abs/2610.19592)
+
+## Download
+
+```bash
+export WORK_ROOT=/path/to/workspace    # default: ~/instructpro2
+huggingface-cli download charlesnovak/InstructPro2 --local-dir $WORK_ROOT/model
+```
+
+## Checkpoints
+
+| File / Directory | Parameters | Use |
+|---|---:|---|
+| `instructpro2_stage1.pt` | 2.87B | Pretrained on InstructPro2Bench. Text-conditioned generation, and the starting point for finetuning. |
+| `instructpro2_stage2_ligand.pt` | 3.22B | Ligand-binding protein design, conditioned on SMILES. |
+| `instructpro2_stage2_antibody.pt` | 3.22B | Antibody design — HCDR1–3 infilling conditioned on an antigen. |
+| `progen2/progen2-large-BFD90/` | 2.7B | Base ProGen2 decoder configuration and weights ([Nijkamp et al., 2023](https://arxiv.org/abs/2206.13517); BSD-3-Clause), used for model initialization and Stage 1 pretraining. |
+
+The Stage 2 checkpoints are larger because they carry the gated cross-attention adapters and the frozen ChemBERTa and ESM-2 encoders.
+
+## Use
+
+Pass a checkpoint to the scripts in the code repository:
+
+```bash
+MODEL_CHECKPOINT=$WORK_ROOT/model/instructpro2_stage1.pt          bash validate_stage1.sh
+MODEL_CHECKPOINT=$WORK_ROOT/model/instructpro2_stage2_ligand.pt   bash eval_ligand.sh
+MODEL_CHECKPOINT=$WORK_ROOT/model/instructpro2_stage2_antibody.pt bash eval_antibody.sh
+```
+
+The scripts set the architecture mode and the generation settings for each checkpoint; see the [code repository's README](https://github.com/chovak/InstructPro2).
+
+## Citation
+
+```bibtex
+@article{instructpro2,
+  title   = {InstructPro2: Natural Language and Biological Grounding Guided De Novo Protein Design},
+  author  = {Charles Novak and Zhenqiao Song and Chuan Li and Jianwen Xie and Lei Li},
+  journal = {arXiv preprint arXiv:2610.19592},
+  year    = {2026}
+}
+```