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

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