---
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](https://github.com/bytedance/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

```bash
# 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.