Datasets:

DeepFoldProtein
/

malidup-dataset

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

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:

@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}
}