This repository contains a crowd sourced list of molecules derived from literature and other sources to aid computational screenings for molecules that have been screened experimentally or computationally against coronaviruses (SARS,MERS, SARS-CoV-2).
/LIT/LIT.csv - A csv file with headers ["molecule", "virus", "reference", "type", "smiles", "pubchem_id", "similarity_calculated", "release"]
- molecule - the name of the molecule (best effort)
- virus - the virus the molecule was screened against (SARS, MERS, SARS-CoV-2)
- reference - the reference from which the information was collected
- type - the type of screening performed ["computational","experimental","mixed"]
- pubchem_smiles - The SMILES as retrieved from pubchem
- canonical_smiles - The oBabel canonical SMILES as computed from the pubchem SMILES
- pubchem_id - The PubChem ID of the molecule if available
- similarity_calculated -
1if similarities have been calculated to other databases,0otherwise - release - The current release associated with the row of information
Note that similarities will be calculated to molecules in the databases available from the The nCov-Group Data Repository, and made available in future releases.
/LIT/references.csv - A line delimited set of references that have been surveyed to arrive at the results
v0.1 (2020-04-21) - initial availability
v0.2 (2020-05-08) - new molecules and inlude Pubchem and canonical SMILES
Yadu Nand Babuji, Ben Blaiszik, Kyle Chard, Ryan Chard, Ian Foster, India Gordon, Zhi Hong, Kasia Karbarz, Zhuozhao Li, Linda Novak, Susan Sarvey, Marcus Schwarting, Julie Smagacz,Logan Ward, Monica Orozco White
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.
Data storage and computational support for this research project has been generously supported by the following resources. The data generated have been prepared as part of the nCov-Group Collaboration, a group of over 200 researchers working to use computational techniques to address various challenges associated with COVID-19.
Petrel Data Service at the Argonne Leadership Computing Facility (ALCF) This research used resources of the Argonne Leadership Computing Facility, a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.
Argonne Leadership Computing Facility (ALCF) This research used resources of the Argonne Leadership Computing Facility, a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.
Frontera at the Texas Advanced Computing Center (TACC)
Comet at the San Diego Supercomputing Center (SDSC)
Data and Computing Infrastructure Many aspects of the data and computing infrastructure have been leveraged from other projects including but not limited to:
Data processing and computation:
- ExaLearn and the Exascale Computing Project
- Parsl: parallel scripting libarary (NSF 1550588)
- funcX: distributed function as a service platform (NSF 2004894)
Data Tools, Services, and Expertise:
- Globus: data services for science (authentication, transfer, users, and groups)
- CHiMaD: Materials Data Facility and Polymer Property Predictor Database (NIST 70NANB19H005 and NIST 70NANB14H012)
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