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--- |
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readme: "true" |
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language: |
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- en |
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tags: |
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- anti-CRISPR |
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- benchmark |
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- Acr |
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task_categories: |
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- text-classification |
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configs: |
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- config_name: default |
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data_files: |
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- split: positive |
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path: "positive.tar.gz" |
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- split: negative |
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path: "negative.tar.gz" |
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--- |
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# ShieldBreaker Benchmark Dataset |
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## Overview |
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The ShieldBreaker Benchmark Dataset is a comprehensive collection of anti-CRISPR protein sequences and structures, designed for machine learning research in CRISPR-Cas system inhibition. This dataset contains both positive (anti-CRISPR) and negative (non-anti-CRISPR) samples with dual-modal data representations. |
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## Dataset Structure |
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``` |
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ShieldBreaker_Upload/ |
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├── positive/ |
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│ ├── fasta/ |
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│ │ └── benchmark_positive_filtered.fasta |
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│ └── pdb/ |
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│ └── [1,421 PDB structure files] |
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├── negative/ |
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│ ├── fasta/ |
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│ │ └── negative_changename_filtered.fasta |
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│ └── pdb/ |
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│ └── [52,824 PDB structure files] |
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└── README.md |
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``` |
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## Data Description |
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### Positive Samples |
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Anti-CRISPR proteins that actively inhibit CRISPR-Cas systems: |
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- **FASTA format**: 1,421 protein sequences with standardized naming convention |
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- **PDB format**: 1,421 corresponding 3D protein structures |
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- **Naming**: `anti_CRISPR{ID}_{Accession}_{AcrFamily}_{Genus}_label_1` or `new_{ID}_{Accession}_{AcrFamily}_{Genus}_label_1` |
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Among these, the naming format starting with new_ refers to newly collected samples based on antiCRISPRdb 2.2 |
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### Negative Samples |
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Non-anti-CRISPR proteins used as negative controls: |
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- **FASTA format**: 52,824 protein sequences (105,648 lines total) |
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- **PDB format**: 52,824 corresponding 3D protein structures |
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- **Naming**: Standardized protein identifiers with label information |
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- **Source**: Carefully selected from all prokaryotic species based on their evolutionary characteristics. |
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## File Formats |
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### FASTA Files |
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- Standard FASTA format with protein sequences |
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- Header information includes accession numbers, protein families, and organism taxonomy |
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- All sequences have been filtered and preprocessed |
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### PDB Files |
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- Protein Data Bank (PDB) format containing 3D atomic coordinates |
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- Standard ATOM records with positions, element types, and connectivity |
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- Each structure corresponds to its respective sequence in the FASTA files |
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- **Prediction Tool**: All PDB structures in this dataset are predicted using ESMFold. |
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## Dataset Statistics |
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| Category | FASTA Files | PDB Files | Total Sequences | |
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| --------- | ----------- | ---------- | --------------- | |
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| Positive | 1 | 1,421 | 1,421 | |
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| Negative | 1 | 52,824 | 52,824 | |
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| **Total** | **2** | **54,245** | **54,245** | |
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## Applications |
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This dataset is designed for: |
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- Anti-CRISPR protein prediction and classification |
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- Machine learning model training and benchmarking |
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- Structure-function relationship analysis |
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- Protein sequence-structure studies |
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- CRISPR-Cas system inhibition research |
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## Usage |
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When using this dataset, please cite the appropriate source and acknowledge that this is a benchmark dataset for anti-CRISPR protein research. |
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## Notes |
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- All protein structures have been preprocessed and standardized |
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- The dataset maintains a 1:1 mapping between FASTA sequences and PDB structures |
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- Negative samples have been curated to provide challenging non-anti-CRISPR examples |
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- Data has been filtered for quality and consistency |
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