Add ProteinMPNN-compatible BindMPNN checkpoints and usage instructions

BindMPNN_soluble_v_48_010.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:cef0372be85f37d280e7c4ce1c3d98875f50345dcccfa98a4a65593d14f469ba
+size 6680267

BindMPNN_soluble_v_48_020.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8ada5ba943c5436873405f0353848c20752fd239b4df883d259acb39e33fdf69
+size 6680267

README.md

@@ -6,14 +6,15 @@ tags:
 - protein-design
 - inverse-folding
 - ligandmpnn
+- proteinmpnn
 - bindmpnn
 ---
 
 # BindMPNN
 
-BindMPNN provides two **LigandMPNN-compatible checkpoints** for amino-acid sequence design from protein structures. Use them with the [official LigandMPNN implementation](https://github.com/dauparas/LigandMPNN) and `--model_type ligand_mpnn`.
+BindMPNN provides **LigandMPNN-compatible and ProteinMPNN-compatible checkpoints** for amino-acid sequence design from protein structures. Use them with the [official LigandMPNN implementation](https://github.com/dauparas/LigandMPNN); the model options and examples for each architecture are given below.
 
-## Checkpoints
+## LigandMPNN-compatible checkpoints
 
 | Checkpoint | Backbone noise level | Protein neighbors | Atom context size |
 |---|---:|---:|---:|
@@ -91,6 +92,49 @@ checkpoint = torch.load(
 # model.load_state_dict(checkpoint["model_state_dict"], strict=True)
 ```
 
+## ProteinMPNN-compatible checkpoints
+
+These additional BindMPNN checkpoints use the **ProteinMPNN architecture** and can be loaded through the `soluble_mpnn` or `protein_mpnn` model options in the official LigandMPNN repository.
+
+| Checkpoint | Backbone noise level | Protein neighbors |
+|---|---:|---:|
+| `BindMPNN_soluble_v_48_010.pt` | 0.10 Å | 48 |
+| `BindMPNN_soluble_v_48_020.pt` | 0.20 Å | 48 |
+
+Download them with:
+
+```python
+from huggingface_hub import hf_hub_download
+
+for filename in ("BindMPNN_soluble_v_48_010.pt", "BindMPNN_soluble_v_48_020.pt"):
+    hf_hub_download(
+        repo_id="MurrellLab/SeqGivenStruct",
+        filename=filename,
+        local_dir="checkpoints",
+    )
+```
+
+Using the same installation described above, redesign chain B while keeping the other chains fixed:
+
+```bash
+python run.py \
+  --model_type soluble_mpnn \
+  --checkpoint_soluble_mpnn checkpoints/BindMPNN_soluble_v_48_010.pt \
+  --pdb_path complex.pdb \
+  --chains_to_design B \
+  --temperature 0.1 \
+  --seed 123 \
+  --batch_size 1 \
+  --number_of_batches 8 \
+  --out_folder outputs/bindmpnn_soluble
+```
+
+Replace the checkpoint filename with `BindMPNN_soluble_v_48_020.pt` for the 0.20 Å variant. Alternatively, use `--model_type protein_mpnn` with `--checkpoint_protein_mpnn` pointing to the same file.
+
+These models use protein backbone coordinates and fixed-chain amino-acid identities. They do **not** accept target side-chain or nonprotein atom context; `--ligand_mpnn_use_side_chain_context` applies only to the LigandMPNN-compatible checkpoints above. Noise labels identify checkpoint variants and are independent of sampling temperature.
+
+For programmatic loading, use `torch.load(path, map_location="cpu", weights_only=True)`, instantiate the upstream `ProteinMPNN` with `model_type="soluble_mpnn"` and `k_neighbors=checkpoint["num_edges"]`, then load `checkpoint["model_state_dict"]` strictly. The files contain only inference weights, `num_edges`, and `noise_level`.
+
 ## Attribution
 
-BindMPNN uses the LigandMPNN architecture and checkpoint format. Please acknowledge [LigandMPNN](https://github.com/dauparas/LigandMPNN) when using these checkpoints.
+Please acknowledge the corresponding upstream implementations: [LigandMPNN](https://github.com/dauparas/LigandMPNN) and [ProteinMPNN](https://github.com/dauparas/ProteinMPNN).

checkpoints.json

@@ -12,5 +12,17 @@
     "num_edges": 32,
     "atom_context_num": 25,
     "noise_level": 0.2
+  },
+  "BindMPNN_soluble_v_48_010.pt": {
+    "sha256": "cef0372be85f37d280e7c4ce1c3d98875f50345dcccfa98a4a65593d14f469ba",
+    "size_bytes": 6680267,
+    "num_edges": 48,
+    "noise_level": 0.1
+  },
+  "BindMPNN_soluble_v_48_020.pt": {
+    "sha256": "8ada5ba943c5436873405f0353848c20752fd239b4df883d259acb39e33fdf69",
+    "size_bytes": 6680267,
+    "num_edges": 48,
+    "noise_level": 0.2
   }
-}
+}