DUDE-Z - the next generation of DUDE

This is DUDE-Z, the the next generation of DUDE

Welcome to DUDE-Z, the next generation of DUDE, a directory of useful decoys. DUDE-Z is designed to help benchmark molecular docking programs by providing challenging decoys. It contains:

DUDE-Z contains property-matched decoys for 43 targets, including 2312 ligands and 69,994 decoys from 33,292 decoy scaffolds. It also contains 732,309 extrema decoys from 143,423 scaffolds and 1,145,472 Goldilocks molecules from 317,316 scaffolds. It also contains a bootstrapping script to assess confidence intervals on docking results. An online decoy-making service is available via http://tldr.docking.org. Login and select Dude. DUDE-Z supercedes previous versions DUD.docking.org and DUDE.docking.org.

DUDE-Z is provided by the Shoichet and Irwin Laboratories in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). To cite DUDE-Z, please cite Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu JK, Young J, Tang K, Shoichet BK and Irwin JJ, J Chem Inf Model, 2021, 61,, 2, 699-714. pubs.acs.org/doi/10.1021/acs.jcim.0c00598

We thank NIGMS for financial support (R01GM71896 to JJI and R35GM122481 to BKS). For correspondence about DUDE-Z, please write John Irwin chemistry 4 biology at gmail dot com.

DUDE-Z may be downloaded target-by-target, or all at once. You may also generate your own decoys.

DUDE-Z is a research tool designed for investigators working with molecular docking. We have tried to make DUDE-Z as useful, correct and easy-to-use as we know how. DUDE-Z is designed for 3D molecular screening methods such as docking and not for 2D methods such as molecular similarity based methods

Anticipating that problems will undoubtedly be found, we have set up a DUDE wiki page and a DUDE Facebook page to allow the community to share problems or observations. We will endeavor to put right any problems promptly, as best we can.

Last updated May 22, 2020

[ICO]NameLast modifiedSizeDescription

[DIR]Charge_matched_DUDE/ 2023-02-17 11:58 -  
[   ]DOCKING_GRIDS_AND_PO..>2023-06-20 20:58 2.2G 
[DIR]DOCKING_GRIDS_AND_PO..>2023-06-20 21:09 -  
[DIR]DUDE-Z-benchmark-grids/2023-02-17 12:05 -  
[DIR]binders_nonbinders/ 2020-05-27 16:33 -  
[   ]bootstrap.tgz 2020-11-24 17:15 397K 
[DIR]bootstrap/ 2020-11-24 17:14 -  
[DIR]extrema/ 2023-02-17 12:02 -  
[DIR]goldilocks/ 2020-05-27 16:37 -  
[DIR]property_matched/ 2023-06-20 19:33 -  
[   ]property_matched_dep..>2023-06-19 19:49 17G 
[DIR]property_matched_dep..>2023-06-19 19:51 -  

More information can go here. --- Ian Scott Knight 2023-06-20 WARNING: `DUDE-Z-benchmark-grids/` should be considered deprecated as I have found it to possess symlinks pointing to non-existent files for many targets. I assume that `DOCKING_GRIDS_AND_POSES/` should be considered the correct version. I recommend that we determine the purpose of `DUDE-Z-benchmark-grids/` and remove to resolve this confusion. ---