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