Datasets:

RosettaCommons
/

NCI_Open_Compounds

language:
  - en
tags:
  - chemistry
  - biology
pretty_name: >-
  Processed NCI Open Compounds Structures for Docking, Cofold, and Affinity
  Prediction
size_categories:
  - 100K<n<1M
configs:
  - config_name: default
    data_files:
      - split: train
        path: nci_compounds.tsv
    delimiter: "\t"

Curated NCI Open Compounds dataset

A curated set of the NCI Open Compounds with compatible mol2 and pdbqt files safe for cofolding and docking applications

Quickstart Usage

Install HuggingFace Datasets package

Each subset can be loaded into python using the Huggingface datasets library. First, from the command line install the datasets library

$ pip install datasets

Optionally set the cache directory, e.g.

$ HF_HOME=${HOME}/.cache/huggingface/
$ export HF_HOME

then, from within python load the datasets library

>>> import datasets

Load model datasets

To load one of the NCI_Open_Compounds model datasets, use datasets.load_dataset(...):

>>> dataset_tag = "train"
>>> dataset_models = datasets.load_dataset(
  path = "leebecca/NCI_Open_Compounds",
  name = f"{dataset_tag}_models",
  data_dir = f"{dataset_tag}")['train']

and the dataset is loaded as a datasets.arrow_dataset.Dataset

>>> dataset_models
Dataset({
    features: [    
      'NSC',
      'duplicate_idx',
      'CID',
      'SID',
      'CAS',
      'entry_id',
      'entry_name',
      'name',
      'formula',
      'smiles',
      'mw',
      'tot_q',
      'tot_abs_q',
      'chiralities_consistent',
      'chiral_flag',
      'flags',
      'charging_adjusted_penalty',
      'ionization_penalty',
      'ionization_penalty_charging',
      'ionization_penalty_neutral',
      'state_penalty',
      'energy',
      'tautomer_probability',
      'input_file',
      'structure_evaluation',
      'chemistry_notes',
      'pka_notes'
    ],
    num_rows: 445794
})

Dataset Details

Dataset Description

The set contains ligprep output of the minimized 3D structures, expanded to include possible protonation states and tautomers capped at 3 per ligand.

Acknowledgements: We kindly acknowledge RosettaCommons

Dataset Sources

https://wiki.nci.nih.gov/spaces/NCIDTPdata/pages/155844992/Chemical+Data

Uses

Out-of-Scope Use

Source Data

Citation

Dataset Card Authors

Becca Lee (beccalee5@g.ucla.edu)