Upload folder using huggingface_hub

README.md

@@ -0,0 +1,65 @@
+---
+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}
+}
+```