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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 (beccalee5@g.ucla.edu) |