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README.md

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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}
+}
+```