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--- |
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pretty_name: MALIDUP |
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language: |
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- en |
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tags: |
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- protein |
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- sequence-alignment |
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- structural-biology |
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- domain-duplication |
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task_categories: |
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- other |
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configs: |
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- config_name: all |
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description: All curated duplicated-domain alignments |
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data_files: |
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- split: test |
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path: all.jsonl |
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--- |
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# MALIDUP (Hugging Face Port) |
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Benchmark of duplicated domain pairs from the same protein chain, curated by structure-based alignment. |
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## Overview |
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- 241 duplicated domain pairs from the same polypeptide chains |
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- Expert-curated alignments based on structural similarity |
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- Useful for evaluating alignment methods under **remote but homologous** scenarios |
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## Features |
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- `pair_id`, `group_id`, `set_name` |
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- `seq1_id`, `seq2_id`, `seq1`, `seq2` |
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- `ref_alignment`: list of aligned residue index pairs (0-based) |
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- `percent_identity`: sequence identity across aligned positions |
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- `scop_labels`: SCOP class, fold, superfamily, family, etc. |
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- `meta`: additional metadata (JSON string) |
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## Usage |
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```python |
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from datasets import load_dataset |
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ds = load_dataset("DeepFoldProtein/MALIDUP", name="all", split="test") |
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ex = ds[0] |
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print(ex["seq1_id"], ex["seq2_id"], ex["ref_alignment"][:5]) |
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``` |
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## Citation |
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Please cite: |
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```bibtex |
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@article{Cheng2007, |
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title = {MALIDUP: A database of manually constructed structure alignments for duplicated domain pairs}, |
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volume = {70}, |
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ISSN = {1097-0134}, |
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url = {http://dx.doi.org/10.1002/prot.21783}, |
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DOI = {10.1002/prot.21783}, |
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number = {4}, |
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journal = {Proteins: Structure, Function, and Bioinformatics}, |
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publisher = {Wiley}, |
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author = {Cheng, Hua and Kim, Bong‐Hyun and Grishin, Nick V.}, |
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year = {2007}, |
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month = oct, |
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pages = {1162--1166} |
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} |
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``` |
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