dud.docking.org

DUD - A Directory of Useful Decoys

A Directory of Useful Decoys. 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. Labs in the Department of Pharmaceutical Chemistry. There is a DUD wiki page.

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DUD - A Directory of Useful Decoys | dud.docking.org Reviews

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A Directory of Useful Decoys. 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. Labs in the Department of Pharmaceutical Chemistry. There is a DUD wiki page.

<META> KEYWORDS

1 and shoichet

2 release

3 date

4 original release

5 proofreading corrections accompanying

6 the final manuscript

7 dud related datasets

8 charge matched dud

9 dud clusters

10 publishers of wombat

CONTENT

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and shoichet,release,date,original release,proofreading corrections accompanying,the final manuscript,dud related datasets,charge matched dud,dud clusters,publishers of wombat,readme file,inhibox website,terms of use,thank you nigms

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DUD - A Directory of Useful Decoys | dud.docking.org Reviews

https://dud.docking.org

A Directory of Useful Decoys. 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. Labs in the Department of Pharmaceutical Chemistry. There is a DUD wiki page.

INTERNAL PAGES

dud.docking.org

1

WOMBAT Data for Enrichment Studies

http://dud.docking.org/wombat

WOMBAT Data for Enrichment Studies. This is the WOMBAT data presented by Andrew Good at the ACS in Boston on August 21, 2007. WOMBAT courtesy of Sunset Molecular. 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. Please direct correspondence to Andrew Good at andrew.good (at) bms dot com cc to jji (at) cgl dot ucsf dot edu.

2

DUD - A Directory of Useful Decoys

http://dud.docking.org/r2

A Directory of Useful Decoys. October 22, 2006. This is release 2, accompanying the publication of the manuscript. See notes accompanying this release. Go back to main DUD page. All DUD Ligand sets (mol2 format). All DUD Decoy sets (mol2 format). All targets (PDB format). Energy scores of all molecules against all targets. All structural ligand controls (mol2 format). All files for all targets. Browse ligands and decoys. Browse the target files. ACE - Angiotensin-converting enzyme. ALR2 - Aldose reductase.

3

Michael Mysinger's Charge-Matched DUD

http://dud.docking.org/charge-matched

Michael Mysinger's Charge-Matched DUD. This is a charge-matched version of DUD, used in our rapid context-dependent ligand-desolvation paper. 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. Please direct correspondence to jji (at) cgl dot ucsf dot edu. Last updated May 25, 2012. Problems with this page to support at docking dot org please.

4

Inhibox Updates Partial Charges in DUD

http://dud.docking.org/inhibox.html

Inhibox Updates Partial Charges in DUD. In a recent paper. ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics. In the Journal of Computer-Aided Molecular Design, a discrepancy between the calculated partial charges for the ligand and decoy data sets of release 2 of the Directory of Useful Decoys. Was reported which made it trivial for virtual screening methods using those charges (. ElectroShape) to distinguish between the two sets.

5

Index of /jmc-water

http://dud.docking.org/jmc-water

Ace 1o86.wat.pdb. Ache 1eve.wat.pdb. Ada 1ndw.wat.pdb. Ampc 1xgj.wat.pdb. Cdk2 1di8.wat.pdb. Comt 1h1d.wat.pdb. Dhfr 3dfr.wat.pdb. Egfr 1xkk.wat.pdb. Fgfr1 1agw.wat.pdb. Fxa 1f0r.wat.pdb. Gart 1c2t.wat.pdb. Gpb 1a8i.wat.pdb. Hivpr 1hpx.wat.pdb. Hmgr 1hw8.wat.pdb. Hsp90 1uy6.wat.pdb. Na 1a4g.wat.pdb. Pde5 1xp0.wat.pdb. Pnp 1b8o.wat.pdb. Sahh 1a7a.wat.pdb. Src 1y57.wat.pdb. Thrombin 1ba8.wat.pdb. Tk 1kim.wat.pdb. Trypsin 1bju.wat.pdb. Vegfr2 1ywn.wat.pdb.

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bcirc.docking.org

BCIRC - A bioinformatics and chemical informatics research center

http://bcirc.docking.org/products.shtml

Crash the entire computer cluster. The Bioinformatics and Chemical Informatics Research Center (BCIRC) develops software tools, databases, and other resources that use chemistry to interpret biology. Currently, we offer several products:. A database of commercially available compounds for virtual screening. Currently version 8 (2008). Version 9 will appear in 2009. A free virtual screening service. Currently in beta test (since Nov 2007). A directory of useful decoys for benchmarking virtual screening.

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DUD - A Directory of Useful Decoys

A Directory of Useful Decoys. 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. Labs in the Department of Pharmaceutical Chemistry. There is a DUD wiki page.

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