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Protocols

Decoys 'R' Us specifications

Information


Unique identifier OMICS_15565
Name Decoys 'R' Us
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Ram Samudrala

Publication for Decoys 'R' Us

Decoys 'R' Us citations

 (3)
call_split

Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms

2013
F1000Res
PMCID: 3892923
PMID: 24555103
DOI: 10.5256/f1000research.2356.r2091
call_split See protocol

[…] abase (a database consisting of high quality structures) - http://kinemage.biochem.duke.edu/databases/top100.php. In order to benchmark model quality assessment programs, we used decoy sets from the Decoys 'R' Us database - http://dd.compbio.washington.edu/. Each set has several structures that are supposed to be ranked worse than the native structure.Structural superimposition has been done usi […]

library_books

Protein structure modelling and evaluation based on a 4 distance description of side chain interactions

2010
BMC Bioinformatics
PMCID: 2912888
PMID: 20624289
DOI: 10.1186/1471-2105-11-374

[…] licability of the developed term for evaluating accuracy of residue-residue interactions in protein structures. We tested the ScSc term for its ability to identify native protein structure within the Decoys 'R' Us decoy sets []. Out of 34 decoy sets, the native structure was ranked first in 29 (Table ). In the remaining 5 cases, two native structures were determined by NMR. The failure of Hunter i […]

library_books

Benchmarking consensus model quality assessment for protein fold recognition

2007
BMC Bioinformatics
PMCID: 2048972
PMID: 17877795
DOI: 10.1186/1471-2105-8-345

[…] eleased into the PDB (as of 26/11/06) were used to provide a common set of models in order to benchmark the performance of each method.In addition, several standard test sets were downloaded from the Decoys 'R' Us [] database (4state_reduced [], lattice_ssfit [] and LMDS []) so that ModFOLD and ModSSEA may be compared with additional published methods. The ability of methods to identify the native […]

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Decoys 'R' Us institution(s)
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA

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