Welcome to DUD, a directory of useful decoys for benchmarking
virtual screening. DUD is designed to help test docking algorithms
by providing challenging decoys. It contains:
- A total of 2,950 active compounds against a total of 40 targets
- For each active, 36 "decoys" with similar physical properties
(e.g. molecular weight, calculated LogP) but dissimilar topology.
DUD is provided by the
Irwin
and
Shoichet labs in the
Department of Pharmaceutical Chemistry at the
University of California, San Francisco (UCSF).
To cite DUD, please reference Huang, Shoichet and Irwin,
J. Med. Chem., 2006, 49(23), 6789-6801.
doi 10.1021/jm0608356.
There is a
DUD wiki page where you can discuss DUD and an
errata page
where problems are reported and explained. We aim to fix all problems in the
next release.
We thank NIGMS for financial support
(GM71896). For correspondence about DUD, please write John Irwin
jji at cgl dot ucsf dot edu.
DUD is drawn from ZINC,
a database of commerically available compounds for virtual screening,
so compounds in DUD are purchasable, although some may become depleted
over time.
You may download DUD either in packages (some of which are large!)
or you may browse the files and download them individually.
Anticipating that problems will be found, and corrected, in DUD,
we number our releases as follows:
| Release | Date | Comments |
|---|
| 1 | Oct 1, 2006 |
Original release |
| 2 |
Oct 22, 2006 |
Proofreading corrections accompanying
the final manuscript. |
DUD-related datasets
| Charge Matched DUD |
Sep 27, 2010 |
Version of DUD adding net charge to the property matching. If you use it, please cite: Mysinger,
M. M.; Shoichet, B. K. "Rapid Context-Dependent Ligand Desolvation in
Molecular Docking" J Chem Inf Model 50:1561-73 (2010). DOI:
10.1021/ci100214a |
| DUD Clusters |
Aug 27, 2007 |
Clustering from Andrew Good presented at the August 2007 ACS meeting |
| WOMBAT Data for Enrichment Studies |
Aug 27, 2007. |
WOMBAT Datasets for Enrichment Studies (presented by Andrew Good at Boston ACS Aug 2007).
WOMBAT courtesy of Sunset Molecular
publishers of WOMBAT.
If you use this data, please cite the following:
Good AC and Oprea TI, "Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?", J. Comput. Aided Mol. Des. 2008, 22: 169-78.
|
| JMC2008-water |
Jun 20, 2008 |
Huang and Shoichet, J Med Chem, 2008, docking with variable water structure |
| DUD LIB VS 1.0 |
Jul 8, 2009 |
DUD subsets for ligand-based virtual screening. Jahn, Hinselmann, Fechner and Zell, "Optimal assignment methods for ligand-based virtual screening",
Journal of Cheminformatics, 2009, 1, 14.
Readme file |
| Partial Charges for DUD Molecules recalculated by Inhibox |
July 13, 2010
|
Local mirror of files
Inhibox website
|
|
