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SARS-CoV2 Docking Dataset

    David M. Rogers | Oak Ridge National Laboratory
    Jens Glaser | Oak Ridge National Laboratory
    Rupesh Agarwal | Oak Ridge National Laboratory
    Josh Vermaas | Oak Ridge National Laboratory
    Micholas Smith | Oak Ridge National Laboratory
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Description

Description: Small-molecule conformations and docking scores for 1.4 billion molecules docked against 6 protein targets from SARS-CoV2: MPro 5R84, MPro 6WQF, NSP15 6WLC, PLPro 7JIR, Spike 6M0J, and a hand-optimized model of the RNA-dependent RNA polymerase. Docking was carried out using the Autodock-GPU program performing 20 independent structure minimizations per dock - saving 3 results per molecule. Scores reported include the Autodock free energy estimate as well as RF3 and VS-DUD-E v2 machine-learned rescoring models. Protein structure files and maps in the format input to Autodock-GPU are included. Literature Ref: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19, J. Chem. Inf. Model. 2020, 60(12): 5832–5852.

Funding Information

DOE Contract Number

DE-AC05-00OR22725

Originating Research Organization

Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Other Contributing Organizations

50159092,50159094,50445429

Sponsoring Organization

Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21);USDOE; ORNL Laboratory Directed Research and Development (LDRD)

Related Works

Details

DOI

https://doi.org/10.13139/OLCF/1783186

Release Date

May 27, 2021

Subject

36 MATERIALS SCIENCE, 59 BASIC BIOLOGICAL SCIENCES, 60 APPLIED LIFE SCIENCES

Keywords

COVID-19, SARS CoV-2, docking, small-molecules

Dataset

Dataset Type

AS Animations/Simulations

Software

python/pandas

Cite This Dataset:

Rogers, D., Glaser, J., Agarwal, R., Vermaas, J., Smith, M., Parks, J., Cooper, C., Sedova, A., Boehm, S., Baker, M., Smith, J. (2021). SARS-CoV2 Docking Dataset. Oak Ridge National Laboratory. https://doi.org/10.13139/OLCF/1783186.

Acknowledgements

This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Advanced Scientific Computing Research programs in the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.