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README_mcpp-dataset.md
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# Unified All-Atom Molecule Generation with Neural Fields — MCPP Dataset
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We curated a dataset of **186,685 MCP–protein complexes** (`mcpp_dataset.tar.gz`) starting from **641 protein–MCP complexes** from the **[RCSB PDB](https://www.rcsb.org/)** using a **“mutate-then-relax”** strategy:
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## Dataset Generation Pipeline
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1. **Mutation:**
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MCPs were randomly mutated at **1 to 8 sites** using **213 distinct amino acids**.
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2. **Relaxation:**
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Mutated complexes were relaxed using **FastRelax in Rosetta**, which iteratively performs side-chain packing and all-atom minimization.
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3. **Selection:**
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The best complexes were chosen based on **lowest interface scores**.
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---
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## Dataset Statistics
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- MCP lengths: **4–25 amino acids** (average 10)
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- **78%** of MCPs contain one or more **non-canonical amino acids**
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---
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## Dataset Splits
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The dataset is split using a clustering-based approach. The **test set** covers **100 protein pockets**:
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| Split | File |
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|---------------|----------------|
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| Training set | `train_data.pt` |
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| Validation set| `val_data.pt` |
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| Test set | `test_data.pt` |
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---
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## How to Use
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1. **Download and extract:**
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```bash
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tar -xvzf mcpp_dataset.tar.gz
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```
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2. **To generate MCP samples with Funcbind, :**
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```bash
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cp train_data.pt val_data.pt test_data.pt mcpp_dataset/
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```
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