HT Docking Data

This site will be updated to include links to the data from our paper.

Data

The data is avilable here via Globus

Top Level Files

The top level direcetory is accessible here: https://app.globus.org/file-manager?origin_id=a386b552-6086-11ea-9688-0e56c063f437&origin_path=%2Fdata%2Fcleaned_docking_dat%2F |Folder | Description| |———— | ————-| |2D | Contains CSV files for each protein indivuidal. They do not contain more data from the aggregated top level ORD and ORZ tables.| |3D | Contains all the SDF files organized by molecular dataset (ORZ or ORD) and protein receptor (in file name). These correspond directly 1-1 to CSV files.| |Models | Contains all the pretrained model files referenced from the paper | |Receptors | Contains all the pdb, receptors, and pdbqt (for AutoDock Vina) which corespond to models and proteins refererenced in filenames and columns from 2D, 3D, and Models folder. |

2D Data

Filename | Description ———— | ————- ord_table.csv | Contains SMILES, TITLE, and docking score against all avilable proteins. Scores are based on Chemgauss4. Molecules from ORD (6M) orz_table.csv | Contains SMILES, TITLE, and docking score against all avilable proteins. Scores are based on Chemgauss4. Molecules from ORZ (6M)

3D structure complexes

The structures are avilable in SDF files here via Globus

Protein Receptors

The protein receptors are available via Globus

Pretrained models

A portion of this data is backup on FigShare

Acknowledgements

• This research was supported by the Exascale Computing Project (17-SC-20-SC), a collaborative effort of the U.S. Department of Energy Office of Science and the National Nuclear Security Administration.

• We acknowledge other members of the National Virtual Biotechnology Laboratory (NVBL) Medical Therapeutics group. We acknowledge computing time via the COVID19 HPC Consortium.

• Research was supported by the DOE Office of Science through the National Virtual Biotechnology Laboratory, a consortium of DOE national laboratories focused on response to COVID-19, with funding provided by the Coronavirus CARES Act. SJ also acknowledges support from ASCR DE-SC0021352.

• Many of the molecular datasets were collected in the following work: Data were collected Targeting SARS-CoV-2 with AI- and HPC-enabled Lead Generation: A First Data Release Yadu Babuji, Ben Blaiszik, Tom Brettin, Kyle Chard, Ryan Chard, Austin Clyde, Ian Foster, Zhi Hong, Shantenu Jha, Zhuozhao Li, Xuefeng Liu, Arvind Ramanathan, Yi Ren, Nicholaus Saint, Marcus Schwarting, Rick Stevens, Hubertus van Dam, Rick Wagner cite this paper

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