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DUD-E specifications


Unique identifier OMICS_02742
Name DUD-E
Alternative name Database of Useful Decoys : Enhanced
Restrictions to use None
Maintained Yes


  • person_outline Brian K. Shoichet

Publication for Database of Useful Decoys : Enhanced

DUD-E citations


Improving Docking Performance Using Negative Image Based Rescoring

Front Pharmacol
PMCID: 5879118
PMID: 29632488
DOI: 10.3389/fphar.2018.00260

[…] ntry System) format using STRUCTCONVERT in MAESTRO 2017-1 (Schrödinger, LLC, New York, NY, USA, 2017). LIGPREP in MAESTRO was used to generate OPLS3 charges and tautomeric states for both the DUD and DUD-E ligand sets at pH 7.4. Next, both of the ligand sets were converted to the SYBYL MOL2 format using MOL2CONVERT in MAESTRO. The back-and-forth conversion between MOL2 and SMILES formats was done […]


Spectrophores as one dimensional descriptors calculated from three dimensional atomic properties: applications ranging from scaffold hopping to multi target virtual screening

J Cheminform
PMCID: 5842169
PMID: 29516311
DOI: 10.1186/s13321-018-0268-9

[…] The DUD-E dataset [, ] was used to evaluate the potential use of spectrophores in the field of virtual screening. The original DUD-E dataset contains a total of 22,886 active compounds for 102 different p […]


An Efficient Implementation of the Nwat MMGBSA Method to Rescore Docking Results in Medium Throughput Virtual Screenings

PMCID: 5844977
PMID: 29556494
DOI: 10.3389/fchem.2018.00043

[…] The AmpC β-lactamase receptor was derived from the 2HDS PDB file (Babaoglu and Shoichet, ) according to what described on the DUD-E website (Mysinger et al., ). Starting from the crystal structure, only chain B was preserved, crystallographic water molecules were removed and the “Structure preparation” module of the MOE soft […]


A Novel Method for Drug Screen to Regulate G Protein Coupled Receptors in the Metabolic Network of Alzheimer's Disease

Biomed Res Int
PMCID: 5838471
PMID: 29675426
DOI: 10.1155/2018/5486403

[…] As the previous description, we perform ILbind-based screen and AutoDock Vina-based screen on each pair of ligand and target in DUD-E dataset listed in , respectively. ILbind scores imply the probability of interaction between ligand and target protein. Meanwhile, AutoDock Vina scores represent the predicted affinity of ligand […]


Decoys Selection in Benchmarking Datasets: Overview and Perspectives

Front Pharmacol
PMCID: 5787549
PMID: 29416509
DOI: 10.3389/fphar.2018.00011
call_split See protocol

[…] Among the recent tools to help create benchmarking sets (MUV, DEKOIS, DUD-E, and MUBD), the main difference resides in the strategy used to achieve their respective objectives: the DUD-E and DEKOIS data sets are designed for evaluating SBVS methods while MUV and MUBD ar […]


Correlation between Virtual Screening Performance and Binding Site Descriptors of Protein Targets

PMCID: 5818911
PMID: 29545955
DOI: 10.1155/2018/3829307

[…] ing functions [–]. However, it has been suggested that the scoring functions performances are target dependent. However, the present study is different in some aspects. The data set is retrieved from DUD-E [] data set to avoid bias in the design of active groups and decoys data set for each protein target. In addition, the protein targets data set is diverse and we attempted to find possible relat […]


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DUD-E institution(s)
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA

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