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OneScience-Group/proteinmpnn

ProteinMPNN Dataset Dataset Description The ProteinMPNN training sample dataset contains PDB-derived structural data for protein sequence design tasks. The data directory is pdb_2021aug02_sample, which contains a structure index table, validation and test cluster split files, and .pt structure tensor files organized by PDB and chain. Supported Tasks This resource is intended for validating training data loading, debugging the training workflow, and… See the full description on the dataset page: https://huggingface.co/datasets/OneScience-Group/proteinmpnn.

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ProteinMPNN Dataset

Dataset Description

The ProteinMPNN training sample dataset contains PDB-derived structural data for protein sequence design tasks. The data directory is pdb_2021aug02_sample, which contains a structure index table, validation and test cluster split files, and .pt structure tensor files organized by PDB and chain.

Supported Tasks

This resource is intended for validating training data loading, debugging the training workflow, and performing minimal data sanity checks for the OneScience/ProteinMPNN model. Model inference generally does not require this training dataset.

Dataset Format and Structure

Path	Description
`pdb_2021aug02_sample/list.csv`	Chain index with the header `CHAINID,DEPOSITION,RESOLUTION,HASH,CLUSTER,SEQUENCE`
`pdb_2021aug02_sample/valid_clusters.txt`	Validation cluster list
`pdb_2021aug02_sample/test_clusters.txt`	Test cluster list
`pdb_2021aug02_sample/pdb/`	PDB-derived `.pt` structure tensor files; the current sample contains 870 `.pt` files

Each chain file typically contains fields such as the amino acid sequence, atomic coordinates, mask, temperature factors, and occupancy.

How to Use the Dataset

Files and Download

bash

hf download --dataset OneScience-Group/proteinmpnn --local-dir ./proteinmpnn_dataset

Training and debugging require the model repository to be prepared separately:

bash

hf download --model OneScience-Group/ProteinMPNN

Data Placement and Validation

It is recommended to use the download directory as the data root:

bash

export DATA_ROOT=/path/to/proteinmpnn_dataset
python tools/validate_dataset.py --data-root .

Example ProteinMPNN training script command:

bash

python train/training.py --path_for_training_data "$DATA_ROOT/pdb_2021aug02_sample" --debug true

The training script is part of the compatible model repository and is not included in this dataset repository.

Official OneScience Information

Platform	OneScience Main Repository	Skills Repository
Gitee	https://gitee.com/onescience-ai/onescience	https://gitee.com/onescience-ai/oneskills
GitHub	https://github.com/onescience-ai/OneScience	https://github.com/onescience-ai/oneskills

Limitations and License

This dataset was curated and converted from wwPDB/PDB biological assemblies and is licensed under CC0-1.0.

Limitations and License

This resource is a sample-scale dataset and does not represent the complete PDB training set. It is intended primarily for ProteinMPNN data loading, training debugging, and workflow sanity checks. When using it, cite the relevant ProteinMPNN papers, upstream projects, and original PDB data sources, and comply with the ModelScope platform rules.