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