| # 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:** |
| MCPs were randomly mutated at **1 to 8 sites** using **213 distinct amino acids**. |
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| 2. **Relaxation:** |
| Mutated complexes were relaxed using **FastRelax in Rosetta**, which iteratively performs side-chain packing and all-atom minimization. |
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| 3. **Selection:** |
| The best complexes were chosen based on **lowest interface scores**. |
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| ## Dataset Statistics |
| - MCP lengths: **4–25 amino acids** (average 10) |
| - **78%** of MCPs contain one or more **non-canonical amino acids** |
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| ## Dataset Splits |
| The dataset is split using a clustering-based approach. The **test set** covers **100 protein pockets**: |
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| | Split | File | |
| |---------------|----------------| |
| | Training set | `train_data.pt` | |
| | Validation set| `val_data.pt` | |
| | Test set | `test_data.pt` | |
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| ## How to Use |
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| 1. **Download and extract:** |
| ```bash |
| tar -xvzf mcpp_dataset.tar.gz |
| ``` |
| 2. **To generate MCP samples with Funcbind, :** |
| ```bash |
| cp train_data.pt val_data.pt test_data.pt mcpp_dataset/ |
