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---
pretty_name: MALISAM
language:
- en
tags:
- protein
- sequence-alignment
- structural-biology
- analog-structures
task_categories:
- other
configs:
- config_name: all
description: All manually aligned structural analogs
data_files:
- split: test
path: all.jsonl
---
# MALISAM (Hugging Face Port)
Benchmark for structural analogs—non-homologous protein motifs with similar 3D structures.
## Overview
- 130 structurally aligned domain pairs with **no evolutionary relationship**
- First benchmark to explicitly evaluate **analog discrimination**
- Alignments are manually curated based on structural similarity alone
## Features
- `pair_id`, `group_id`, `set_name`
- `seq1_id`, `seq2_id`, `seq1`, `seq2`
- `ref_alignment`: list of residue index pairs (0-based)
- `percent_identity`: sequence identity across aligned residues
- `scop_labels`: optional (typically empty for MALISAM)
- `meta`: optional notes extracted from original text files
## Usage
```python
from datasets import load_dataset
ds = load_dataset("DeepFoldProtein/MALISAM", name="all", split="test")
ex = ds[0]
print(ex["pair_id"], ex["ref_alignment"][:5])
```
## Citation
```bibtex
@article{Cheng2007MALISAM,
title = {MALISAM: a database of structurally analogous motifs in proteins},
volume = {36},
ISSN = {1362-4962},
url = {http://dx.doi.org/10.1093/nar/gkm698},
DOI = {10.1093/nar/gkm698},
number = {Database},
journal = {Nucleic Acids Research},
publisher = {Oxford University Press (OUP)},
author = {Cheng, H. and Kim, B.-H. and Grishin, N. V.},
year = {2007},
month = dec,
pages = {D211--D217}
}
```
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