AMP Project Data

# AMP Dataset Documentation

This repository contains several datasets used for conducting ProteoGPT, AMPSorter, AMPGenix and BioToxiPept and datasets conducted with prediction results. Below is a description of each dataset included in this repository.

## Datasets

### 1. `uniprot-compressed_true_download_true_format_fasta_includeIsoform_tr-2022.10.13-02.51.31.70.fasta`
- **Description**: 609,216 non-redundant canonical and isoform protein sequences.

### 2. `protein_seqs_1000.json`
- **Description**: Contains the training data for ProteoGPT.

### 3. `amp_unique_16062.json`
- **Description**: Contains the training data for AMPGenix.

### 4. `AMPSorter&BioToxiPept dataset.xlsx`
- **Description**: Contains the fine-tuning data, including:
  - **AMP_data split**: Data used for training,  validating and  evaluating AMPSorter.
  - **AMP_test Set**: Data used for test AMPSorter.
  - **AMP_benchmarking Set**: A set of peptides used for benchmarking the AMP models.
  - **AMP_external Validation Dataset**: A separate dataset for external model validation for AMPSorter.
  - **Toxin_data split**: Data used for training,  validating and  evaluating BioToxiPept.
  - **Toxin_test set**: A set of peptides used for testing the toxin models.

### 5. `NRSPDs`
- **Description**: A large dataset that includes:
  - **410,192,277 non-redundant short peptides**.
  - **A candidate pool of 82,694,928 peptides**.
  - **Logits** with results predicted by  AMPsorter and BioToxiPept.

### 6. `GNRSPDs`
- **Description**: Contains:
  - **7,798 generated sequences**.
  - **A candidate pool of 4,736 peptides**.
  - **Logits**with results predicted by  AMPsorter and BioToxiPept.

### 7. `196 tested peptides.xlsx`
- **Description**: A set of  196 selected and experimentally tested peptides, with experimentally measured values.

### 8. `20 pilot tested peptides.xlsx`
- **Description**: 20 selected  peptides with prediction results and experimentally values measured in pilot test.

### 9. `Sequences generated by different models.xlsx`
- **Description**: Sequences generated by different models with prediction results.