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