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DUD-E: A Database of Useful (Docking) Decoys — Enhanced

A Database of Useful Decoys: Enhanced. Welcome to DUD•E. An enhanced and rebuilt version of DUD, a directory of useful decoys. DUD-E is designed to help benchmark molecular docking programs by providing challenging decoys. It contains:. 22,886 active compounds and their affinities against 102 targets, an average of 224 ligands per target. 50 decoys for each active having similar physico-chemical properties but dissimilar 2-D topology. DUD-E is a collaboration of the Irwin. To cite DUD-E, please reference.

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DUD-E: A Database of Useful (Docking) Decoys — Enhanced | dude.docking.org Reviews

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A Database of Useful Decoys: Enhanced. Welcome to DUD•E. An enhanced and rebuilt version of DUD, a directory of useful decoys. DUD-E is designed to help benchmark molecular docking programs by providing challenging decoys. It contains:. 22,886 active compounds and their affinities against 102 targets, an average of 224 ligands per target. 50 decoys for each active having similar physico-chemical properties but dissimilar 2-D topology. DUD-E is a collaboration of the Irwin. To cite DUD-E, please reference.

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4 generate

5 revisions

6 thanks

7 and shoichet

8 we thank nigms

9 organized by subset

10 decoys

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DUD-E: A Database of Useful (Docking) Decoys — Enhanced | dude.docking.org Reviews

https://dude.docking.org

A Database of Useful Decoys: Enhanced. Welcome to DUD•E. An enhanced and rebuilt version of DUD, a directory of useful decoys. DUD-E is designed to help benchmark molecular docking programs by providing challenging decoys. It contains:. 22,886 active compounds and their affinities against 102 targets, an average of 224 ligands per target. 50 decoys for each active having similar physico-chemical properties but dissimilar 2-D topology. DUD-E is a collaboration of the Irwin. To cite DUD-E, please reference.

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dude.docking.org

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Acknowledgements | DUD-E: A Database of Useful (Docking) Decoys — Enhanced

http://dude.docking.org/thanks

A Database of Useful Decoys: Enhanced. DUD-E would not be possible without the help of our colleages. Teague Sterling, for website programming. ChEMBL, the medicinal chemistry database, https:/ www.ebi.ac.uk/chembldb/. ChemAxon, for fingerprints and other tools, http:/ chemaxon.com. OpenEye Scientific Software, for OEChem and Omega, http:/ eyesopen.com. Schrodinger, for Epik, http:/ schrodinger.com. Andrew Good, for early expert feedback. For financial support (GM71896 to BKS and JJI).

2

Generate Decoys | DUD-E: A Database of Useful (Docking) Decoys — Enhanced

http://dude.docking.org/generate

A Database of Useful Decoys: Enhanced. Generate DUD•E Decoys. To generate decoys for your active compounds, use our free on-line system below. Here is how:. Paste a list of SMILES in the window below or choose a text files to upload. In each case, the format is one SMILES per line, optionally followed by white space and an identifer. Anonymous users must complete a CAPTCHA. To use your docking.org account. Human Test: How are you today? Input SMILES by pasting OR uploading a text file.

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Subsets | DUD-E: A Database of Useful (Docking) Decoys — Enhanced

http://dude.docking.org/subsets

A Database of Useful Decoys: Enhanced. DUD•E free to use and is provided by the Irwin and Shoichet Laboratories at UCSF. To cite DUD•E, please reference. Mysinger MM, Carchia M, Irwin JJ, Shoichet BK J. Med. Chem. 2012, Jul 5. doi 10.1021/jm300687e. You may also wish to cite the original version of DUD, Huang, Shoichet and Irwin, J. Med. Chem. 2006, 49(23), 6789-6801. doi 10.1021/jm0608356.

4

Revisions | DUD-E: A Database of Useful (Docking) Decoys — Enhanced

http://dude.docking.org/revisions

A Database of Useful Decoys: Enhanced. DUD•E Revisions and History. DUD-E revision history and archived releases. May 18th, 2012. Initial Release, for review. DUD•E free to use and is provided by the Irwin and Shoichet Laboratories at UCSF. To cite DUD•E, please reference. Mysinger MM, Carchia M, Irwin JJ, Shoichet BK J. Med. Chem. 2012, Jul 5. doi 10.1021/jm300687e. You may also wish to cite the original version of DUD, Huang, Shoichet and Irwin, J. Med. Chem.

5

All Targets | DUD-E: A Database of Useful (Docking) Decoys — Enhanced

http://dude.docking.org/targets

A Database of Useful Decoys: Enhanced. DUD-E contains 102 targets, including 38 of the original 40 DUD targets. Here, you may browse the target and download files by clicking on its gene name, or sort by a column by clicking on its title. To download all of DUD-E, please use the Download Subsets. Tab To make your own decoys, use the Generate. Tab For documentation and discussion, see the DUDE wiki page. Macrophage colony stimulating factor receptor. C-X-C chemokine receptor type 4. Focal adhesion kinase 1.

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http://irwinlab.compbio.ucsf.edu/projects

University of California, San Francisco. Irwin Lab @ UCSF. We are currently working on the following projects. ZINC 12 is a widely used tool for finding purchasable compounds along with 3D structures for docking. ZINC 15 is a completely re-tooled and much more powerful version coming soon. DOCK Blaster is a public access, web-based target-based virtual screening system. We developed DUD-E, an enhanced version of DUD, to benchmark molecular docking library screens. Pharmacology for Cancer Genomics.

wiki.bkslab.org

DUD - DISI

http://wiki.bkslab.org/index.php/DUD

A directory of universal decoys (DUD). The DUD paper was published in J Med Chem, appearing on ASAP October 25-26th. We think DUD might be useful as part of a Docking Competition. This wiki page may be used to discuss DUD and to report results. We welcome all helpful feedback. If you find problems with DUD, please tell John Irwin, but you may also want to point out these problems here. This is really a forum for DUD users to share their experiences. Log in / create account.

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DUD-E: A Database of Useful (Docking) Decoys — Enhanced

A Database of Useful Decoys: Enhanced. Welcome to DUD•E. An enhanced and rebuilt version of DUD, a directory of useful decoys. DUD-E is designed to help benchmark molecular docking programs by providing challenging decoys. It contains:. 22,886 active compounds and their affinities against 102 targets, an average of 224 ligands per target. 50 decoys for each active having similar physico-chemical properties but dissimilar 2-D topology. DUD-E is a collaboration of the Irwin. To cite DUD-E, please reference.

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