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WHISCY specifications

Information


Unique identifier OMICS_08140
Name WHISCY
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Version 1.02
Stability Stable
Maintained Yes

Publication for WHISCY

WHISCY in publications

 (6)
PMCID: 4329070
PMID: 25546632
DOI: 10.1002/prot.24751

[…] then was refined by means of restrained docking calculations that included information about the interacting surfaces. in particular, ambiguous interaction restraints (airs) were defined between the whiscy-predicted interface residues of ec-ymdb (supporting information ) and residues 120–140 of both riiid subunits of the ec-rnase iii holoenzyme. the 120–140 segment of rnase iii […]

PMCID: 3983112
PMID: 24722547
DOI: 10.1371/journal.pone.0093709

[…] protein structures , which may be used as complementary tools to our simulations. several web servers are available for this purpose (cons-ppisp , pier , consurf , promate , prism , sppider and whiscy ). we selected sppider based on its superior performance in comparison to other servers . in this work, we used sppider i with the tradeoff parameter of 0.3 to predict the residues […]

PMCID: 3919607
PMID: 24234454
DOI: 10.1093/nar/gkt1091

[…] code 2ale) using the haddock 2.1/cns 1.21 protocol (). to this end, we first identified the snu13p active residues (according to the haddock nomenclature) () by (i) high prediction scores from both whiscy and promate programs (,); (ii) high solvent accessibility; (iii) spatial proximity; and (iv) taking into account residues found to play key roles in the interaction by experimental assays. […]

PMCID: 4393060
PMID: 25937947
DOI: 10.1155/2013/437168

[…] by structural features including secondary structure, solvent accessibility, and depth []., the interfacial amino acids participating in the protein-protein interaction were enumerated using whiscy [] and predus [] programs, respectively. both of these programs utilize structural conservativeness as the main stream for prediction wherein whiscy considers surface smoothing […]

PMCID: 2894039
PMID: 20507585
DOI: 10.1186/1471-2105-11-286

[…] - 70% success rate (on 51 protein structures) has been reported []. promate has also been combined with another prediction program based on surface conservation and structural information (whiscy) []. the algorithm implemented in whiscy uses a sequence alignment to calculate a prediction score (the residue is predicted as "interface" if the score exceeds a certain threshold) […]


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WHISCY institution(s)
Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands

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