# ProteinMPNN Execution Guide

![The flow](images/ProteinMPNN_1.png)

ProteinMPNN is a tool for protein sequence design based on backbone structures. Follow these steps on an E2E GPU Node.

## Step 1: Clone Repository

```bash
git clone https://github.com/dauparas/ProteinMPNN.git
cd ProteinMPNN
```

## Step 2: Create Environment

```bash
conda create --name mlfold
source activate mlfold
```

## Step 3: Install Dependencies

**For CPU:**

```bash
pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
```

**For GPU:**

```bash
pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu121
conda install cudatoolkit=11.3
```

## Step 4: Load Model

Update paths and load the pretrained weights:

```bash
path_to_model_weights=/mnt/model/vdb/ProteinMPNN/vanilla_model_weights
model_name="v_48_020"
checkpoint_path=$path_to_model_weights/$model_name.pt
```

Example in Python:

```python
import torch
from protein_mpnn_utils import ProteinMPNN

device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
checkpoint = torch.load(checkpoint_path, map_location=device)
model = ProteinMPNN(num_letters=21, hidden_dim=128, num_encoder_layers=3, num_decoder_layers=3)
model.load_state_dict(checkpoint['model_state_dict'])
model.to(device).eval()
print("Model loaded")
```

## Step 5: Run Design

Provide a PDB file and specify designed/fixed chains.

Example:

```python
pdb_path = "/mnt/model/vdb/ProteinMPNN/inputs/PDB_monomers/pdbs/5L33.pdb"
designed_chain = "A"
fixed_chain = ""
```

Adjust design options such as:

```python
num_seqs = 1
sampling_temp = 0.1
batch_size = 1
```

Run the script to generate designed sequences.

## Step 6: Output Results

The tool outputs designed sequences in FASTA format with scores and sequence recovery rates.

**Example output:**

```plaintext
>5L33, score=1.6044, designed_chains=['A'], model_name=v_48_020
HMPEEEKAARLFIEALEK...
```

## Examples of PDBs

You can find Protein Data Bank (PDB) files at the following sources:

- [RCSB PDB Monomers](https://www.rcsb.org/)
- [CASP14 Target 41](https://predictioncenter.org/casp14/)

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---

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