---
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}
}
```