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--- |
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tags: |
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- casp |
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- protein_structure_prediction |
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pretty_name: CASP |
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size_categories: |
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- n<1K |
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--- |
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# CASP Dataset |
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This dataset contains protein structure prediction data compiled from the Critical Assessment of Structure Prediction (CASP) experiments for years 14, 15, and 16. The data is primarily organized for single-chain protein structure prediction testing. |
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## Dataset Overview |
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The dataset includes experimental data from three CASP competitions: |
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- **CASP14** (2020) |
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- **CASP15** (2022) |
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- **CASP16** (2024) |
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## Directory Structure |
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``` |
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casp_data/ |
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├── casp14/ |
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│ ├── sequences.fasta |
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│ ├── experiment_structures/ |
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│ │ ├── T1024.pdb |
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│ │ ├── T1030.pdb |
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│ │ ├── T1032.pdb |
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│ │ ├── T1034.pdb |
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│ │ ├── T1038.pdb |
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│ │ ├── T1046s1.pdb |
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│ │ ├── T1046s2.pdb |
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│ │ └── ... |
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│ └── precomputed_msa/ |
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│ ├── T1024/ |
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│ │ └── non_pairing.a3m |
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│ ├── T1030/ |
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│ │ └── non_pairing.a3m |
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│ └── ... |
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├── casp15/ |
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│ ├── sequences.fasta |
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│ ├── experiment_structures/ |
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│ │ └── [PDB files] |
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│ └── precomputed_msa/ |
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│ └── [MSA directories] |
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└── casp16/ |
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├── sequences.fasta |
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├── experiment_structures/ |
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│ └── [PDB files] |
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└── precomputed_msa/ |
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└── [MSA directories] |
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``` |
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## File Descriptions |
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### `sequences.fasta` |
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Contains all target protein sequences for the respective CASP competition in FASTA format. Each sequence corresponds to a prediction target with identifiers like T1024, H1151s1, etc. |
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### `experiment_structures/` |
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Directory containing experimentally determined protein structures in PDB format. These serve as ground truth structures for evaluating prediction accuracy. Files are named according to their CASP target identifiers (e.g., `T1024.pdb`). |
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### `precomputed_msa/` |
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Contains precomputed Multiple Sequence Alignments (MSA) for each target, organized in subdirectories by target ID. Each subdirectory contains: |
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- `non_pairing.a3m`: MSA file in A3M format |
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## MSA Generation Details |
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The Multiple Sequence Alignments were generated using MMseqs2 with ColabFold scripts, searching against the following databases: |
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- **uniref30_2302_db**: UniRef30 database |
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- **colabfold_envdb_202108_db**: ColabFold environmental database |
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The MSA generation command used: |
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```bash |
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--db1 uniref30_2302_db \ |
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--db3 colabfold_envdb_202108_db |
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``` |
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## Usage |
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This dataset is suitable for: |
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- Evaluating deep learning models for protein structure prediction |
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## Data Attribution |
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All data in this repository is sourced from publicly available databases and competitions: |
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- **CASP (Critical Assessment of protein Structure Prediction)**: Protein structure prediction targets and evaluation data from the CASP website (https://predictioncenter.org/) |
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- **PDB (Protein Data Bank)**: Experimental protein structures from the RCSB Protein Data Bank (https://www.rcsb.org/) |
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We have organized and compiled this data for research purposes. All rights remain with the original data providers and owners. This repository does not claim ownership of any original data - we simply provide an organized collection for convenience. |
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### Original Data Sources: |
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- CASP competition data: © CASP organization |
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- PDB structures: © RCSB Protein Data Bank and original depositors |
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Please cite the original sources when using this data in your research. |
