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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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-
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- ## Dataset Generation Pipeline
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-
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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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-
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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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-
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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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- ---
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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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- ---
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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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-
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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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- ---
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-
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- ## How to Use
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-
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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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- ```