Datasets:

DeepFoldProtein
/

malisam-dataset

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

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

@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}
}