Welcome to Screening Databases

This page contains covalent docking libraries of commercially available compounds developed for two papers:

Mpro paper

Elissa A. Fink, Conner Bardine, Stefan Gahbauer, Isha Singh, Kris White, Shuo Gu, Xiaobo Wan, Beatrice Ary, Isabella Glenn, Joseph O'Connell, Henry O'Donnell, Pavla Fajtova, Jiankun Lyu, Seth Vigneron, Nicholas J. Young, Ivan S. Kondratov, Anthony J. O'Donoghue, Yurii Moroz, Jack Taunton, Adam R. Renslo, John J. Irwin, Adolfo García-Sastre, Brian K. Shoichet, Charles S Craik, Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors, bioRxiv 2022.07.05.498881; doi:

Nsp14 paper

Isha Singh, Fengling Li, Elissa Fink, Irene Chau, Alice Li, Annia Rodriguez-Hernandez Isabella Glenn, Francisco J. Zapatero-Belinchón, Mario Rodriguez, Kanchan Devkot, Zhijie Deng, Kris White, Xiaobo Wan, Nataliya A. Tolmachova, Yurii S. Moroz, H. Umit Kaniskan, Melanie Ott, Adolfo Gastía-Sastre, Jian Jin, Danica Galoic Fujimori, John J. Irwin, Masoud Vedadi, Brian K. Shoichet, Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14 N7-methyltransferase bioRxiv 2023.01.12.523677; doi:

The databases below are free to download. If you use them, please cite the relevant paper.

This work comes to you from the Shoichet Laboratory at UCSF. Full lab Publications

These libraries are free to use, but you must use them at your own risk.

Nitriles for Mpro

In 2D:
(smiles pending) 

In 3D:
bash get_nitrile2_leads_3d.cmd

bash get_nitrile2_fragments_3d.cmd

Acrylamides for Nsp14

In 2D: (17,526,957 molecules)

In 3D: (17,713 db2.gz files total)
bash get_acrylamides_3d.cmd

Aldehydes for Mpro 2020

In 2D: (2,510,964 molecules) 

In 3D:  (2083 db2.gz fragment files and 28878 db2.gz leadlike files)
bash get_aldehydes_2020_fragments_3d.cmd

bash get_aldehydes_2020_leadlike_3d.cmd

Ketoamides for Mpro

In 2D: (1,521,347 molecules)

In 3D: (5819 db2.gz files)
bash get_ketoamides_3d.cmd

Aldehydes for Nsp14 2021

In 2D: (4,729,871 molecules)

in 3D: (4728 db2.gz files)
bash get_aldehydes_2021_fragments_3d.cmd
Last updated: Mar 17, 2023 by John Irwin
[ICO]NameLast modifiedSizeDescription

[   ]acrylamides.smi.gz 2023-03-15 16:42 257M 
[   ]aldehydes_nsp14_2021..>2023-03-15 16:45 37M 
[   ]aldehydes_mpro_2020...>2023-03-15 16:44 35M 
[   ]ketoamides.smi.gz 2023-03-17 10:45 14M 
[   ]get_aldehydes_2020_3..>2023-03-15 16:47 3.3M 
[   ]get_aldehydes_2020_l..>2023-03-15 21:22 3.1M 
[   ]get_acrylamides_3d.cmd 2023-03-15 16:39 1.7M 
[   ]get_nitrile2_fragmen..>2023-03-16 19:31 1.0M 
[   ]get_nitrile2_leads_3..>2023-03-16 19:32 812K 
[   ]get_aldehydes_2021.cmd 2023-03-15 21:29 503K 
[   ]get_ketoamides_3d.cmd 2023-03-16 19:49 496K 
[   ]get_aldehydes_2021_3..>2023-03-15 21:30 443K 
[   ]get_nitriles1_3d.cmd 2023-03-16 19:38 275K 
[   ]get_aldehydes_2020_f..>2023-03-15 21:22 235K 
[DIR]nitriles2/ 2020-03-29 22:34 -  
[DIR]nitrile2-leads/ 2020-04-15 11:55 -  
[DIR]nitrile2-fragments/ 2020-07-01 11:28 -  
[DIR]ketoamides/ 2020-03-27 16:48 -  
[DIR]aldehydes_2021/ 2022-05-10 11:23 -  
[DIR]aldehydes_2020_leadl..>2020-04-01 12:26 -  
[DIR]aldehydes_2020_fragm..>2020-04-03 12:12 -  
[DIR]aldehydes/ 2020-03-17 17:31 -  
[DIR]acrylamides/ 2023-03-14 22:00 -  

This space reserved for future files to be downloaded. For now, please use the tranche browsers referenced above.