# PockLigGPT

PockLigGPT is a pocket-conditioned molecular generation framework based on GPT architectures and reinforcement learning (RL) for structure-based drug design.

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## 🌐 Access & Resources

### 🔬 Web Interface
👉 https://pockliggpt.streamlit.app  

Researchers and companies can:
- submit PDB structures  
- request molecule generation  
- request full computational studies  

### 💻 Code
👉 https://github.com/pvaras8/PockLigGPT_official  

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## 🧬 Key Features

- 🧠 **Protein-conditioned generation** using sequence + embeddings  
- 🧪 **Docking-aware optimization** via reinforcement learning  
- 🔬 **Structure-based drug design pipeline** end-to-end  
- ⚡ **Scalable GPT-based architecture** for molecular generation  

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## 📦 Available Models

### Pretraining
- `ckpt_zink_M.pt` → ZINC pretraining  
- `ckpt_zink_chembl.pt` → ZINC + ChEMBL pretraining  

### Fine-tuned (CrossDocked)
- `ckpt_zink_chembl_cross_sequence_add.pt` → enhanced conditioning  

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## 🚀 What Can It Do?

PockLigGPT enables:

- Generation of novel molecules conditioned on protein pockets  
- Optimization of binding affinity using RL + docking  
- Exploration of chemical space under structural constraints  
- End-to-end workflows for early-stage drug discovery  

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## 🧪 Example Workflow

1. Load a pretrained checkpoint  
2. Provide protein pocket:
   - amino acid sequence  
   - ProtT5 embeddings  
   - docking grid  
3. Run RL optimization  
4. Generate candidate molecules  

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## ⚙️ Technical Stack

- SELFIES molecular representation  
- GPT-based autoregressive models  
- ProtT5 protein embeddings  
- AutoDock Vina (reward signal)  
- Reinforcement learning (PPO-style)  

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## 💼 Commercial Use

PockLigGPT is available for research use.

For:
- industrial applications  
- large-scale screening  
- full structure-based optimization workflows  

👉 please contact via the web interface.

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## ⚠️ Limitations

- RL requires docking setup (external tools)  
- Computationally intensive for large-scale runs  
- Requires protein preprocessing  

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## 📜 License

MIT License  

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## 📄 Citation

Coming soon