Hugging Face's logo

Datasets:
Windsao
/
anewomni-train-data

Tasks:
Other
Tags:
protein-ligand
structure-based-drug-design
molecular-generation
anewomni
License:
Dataset card Files
xet
 Community
anewomni-train-data / README.md
Windsao's picture
Windsao
Upload README.md with huggingface_hub
b7bf7e8 verified
preview code
|
Raw
History Blame Contribute Delete
3.38 kB
metadata 
license: cc-by-4.0
task_categories:
  - other
tags:
  - protein-ligand
  - structure-based-drug-design
  - molecular-generation
  - anewomni
pretty_name: AnewOmni Training Datasets (non-SIU)

AnewOmni Training Datasets — non-SIU subset

Preprocessed, training-ready datasets for AnewOmni ("Programming Biomolecular Interactions with an All-Atom Generative Model"), in the codebase's memory-mapped format (data.bin + index.txt + split/cluster index files).

This bundle holds 7 of the 8 training sources — everything except SIU (SIU is ~156 GB and is distributed separately). After extraction the datasets/ tree matches the paths in configs/train_ldm.yaml / configs/train_vae.yaml with 0 missing files.

Contents

Dataset Modality Entries Splits Original source
PepBench peptide 6,105 train 4,157 / valid 114 (LNR 93 test held out) Zenodo 13373108 (PepGLAD)
ProtFrag peptide (augmentation) 70,498 — Zenodo 13373108 (PepGLAD)
SAbDab antibody 16,947 train 9,473 / valid 400 OPIG / UniMoMo
PDBbind v2020 small molecule 16,200 refined 4,628 (+train/valid) + other-PL 11,572 PDBbind v2020
BioLiP2-nr small molecule 51,114 pretrain / finetune (by resolution) zhanggroup.org/BioLiP
CrossDocked2020 small molecule 100,081 train 99,881 / valid 100 / test 100 TargetDiff Google Drive
SIU (separate upload) small molecule 4,289,980 cluster-weighted HuggingFace bgao95/SIU

Bundle total: ~261k entries, 17.2 GB (anewomni_datasets_noSIU.tar).

Usage 

# on your training server, from the AnewOmni repo root:
hf download Windsao/anewomni-train-data anewomni_datasets_noSIU.tar --repo-type dataset --local-dir .
tar -xf anewomni_datasets_noSIU.tar        # -> ./datasets/...
rm anewomni_datasets_noSIU.tar

The extracted layout:

datasets/
  peptide/pepbench/processed/        (+ ../train.cluster)
  peptide/ProtFrag/processed/
  antibody/SAbDab/processed/
  molecule_v2/PDBbind/processed/{refined-set,v2020-other-PL}/
  molecule_v2/biolip2_nr/processed/
  molecule_v2/CrossDocked/processed/

Format

Each dataset is a memory-mapped store:

  • data.bin — concatenated, per-entry zlib-compressed complexes (receptor + binder).
  • index.txt — one line per entry: id \t start \t end \t properties-json (byte range [start,end) into data.bin).
  • *_index.txt — train / valid / test subsets (an entry list).
  • *.cluster — sequence / scaffold clusters used for size- and redundancy-aware sampling.

Loadable via the AnewOmni MoleculeDataset / PeptideDataset / AntibodyDataset classes (mmap_dir=…, specify_index=…, cluster=…).

Notes

  • Counts are from raw processing of each source. The AnewOmni paper applies an additional ligand-quality filtering pipeline (CCD exclusion list, cross-source dedup by PDB code, 40% sequence-identity train/test cutoff) that is not applied here — so the small-molecule counts above are somewhat higher than the paper's final training numbers (PDBbind 14,200 / BioLiP2 18,012 / CrossDocked 85,938). PepBench (4,157) and SAbDab (9,473/400) splits match the paper exactly.
  • Derived from publicly available datasets (mostly CC-BY); refer to each original source for its license.