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](https://huggingface.co/docs/datasets/index) 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 ([e-mail])