SARS-CoV2 Docking Dataset

10.13139/OLCF/1783186

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.

Published: 2021-05-27 10:57:05 Download Dataset

Dataset Properties

Field Value
Authors
  • Rogers, David M. Oak Ridge National Laboratory
  • Glaser, Jens Oak Ridge National Laboratory
  • Agarwal, Rupesh Oak Ridge National Laboratory
  • Vermaas, Josh Oak Ridge National Laboratory
  • Smith, Micholas Oak Ridge National Laboratory
  • Parks, Jerry Oak Ridge National Laboratory
  • Cooper, Connor Oak Ridge National Laboratory
  • Sedova, Ada Oak Ridge National Laboratory
  • Boehm, Swen Oak Ridge National Laboratory
  • Baker, Matthew Oak Ridge National Laboratory
  • Smith, Jeremy Oak Ridge National Laboratory
Project Identifier 32102676
Dataset Type AS Animations/Simulations
Subjects
  • 36 MATERIALS SCIENCE
  • 59 BASIC BIOLOGICAL SCIENCES
  • 60 APPLIED LIFE SCIENCES
Keywords
  • COVID-19
  • SARS CoV-2
  • docking
  • small-molecules
Software Needed python/pandas
Originating Organizations Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organizations Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21);USDOE; ORNL Laboratory Directed Research and Development (LDRD)
DOE Contract DE-AC05-00OR22725
Related Identifiers
  • Cites (DOI) 10.1021/acs.jcim.0c01010
  • IsSupplementedBy (DOI) 10.13139/OLCF/1650650
  • IsSupplementedBy (DOI) 10.13139/OLCF/1657844
  • IsSupplementedBy (DOI) 10.13139/OLCF/1657847

Acknowledgements

Papers using this dataset are requested to include the following text in their acknowledgements:

*Support for 10.13139/OLCF/1783186 is provided by the U.S. Department of Energy, project 32102676 under Contract DE-AC05-00OR22725. This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility.