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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 citations

 (8)
library_books

Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB

2015
Proteins
PMCID: 4329070
PMID: 25546632
DOI: 10.1002/prot.24751

[…] E162 (Supporting Information ). Of these, G32, G124, V125, and Y126 also are located near the postulated ADPR binding site. Interestingly, three of the residues (G32, R40, and Y126) are predicted by WHISCY to be important for protein-protein interactions (Supporting Information ). For the RIIID (and the symmetry-related RIIID′), five of the ten top residues (R11, Y15, T16, N18, and R59) are locat […]

library_books

The Interaction of CRM1 and the Nuclear Pore Protein Tpr

2014
PLoS One
PMCID: 3983112
PMID: 24722547
DOI: 10.1371/journal.pone.0093709

[…] d/or 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 in the comp […]

library_books

Characterization of the interaction between protein Snu13p/15.5K and the Rsa1p/NUFIP factor and demonstration of its functional importance for snoRNP assembly

2013
Nucleic Acids Res
PMCID: 3919607
PMID: 24234454
DOI: 10.1093/nar/gkt1091

[…] B 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. Snu1 […]

library_books

Structural Bioinformatics and Protein Docking Analysis of the Molecular Chaperone Kinase Interactions: Towards Allosteric Inhibition of Protein Kinases by Targeting the Hsp90 Cdc37 Chaperone Machinery

2013
PMCID: 3854018
PMID: 24287464
DOI: 10.3390/ph6111407

[…] unctional role that could be tailored for general recognition of kinase folds and specific regulatory functions. A panel of various protein-protein interaction predictor methods including ProMate [], WHISCY [], Consurf [], InterProSurf [], PPI-Pred [], and SPPIDER [] was used to build a consensus scoring of probable interfacial residues [] for the kinase clients and the Cdc37 chaperone. The crysta […]

library_books

Structures of Saccharomyces cerevisiae d arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor assisted substrate recognition

2013
PMCID: 3818031
PMID: 24192347
DOI: 10.1107/S1744309113026857

[…] of Ara1–NADPH using HADDOCK (de Vries et al., 2010). The docking program was driven by interaction restraints between the active-site residues of Ara1 and the α,β-dicarbonyl substrate, as defined by WHISCY (Adams et al., 2002) and previously reported by Jez et al. (1997). Docking produced 25 clusters for diacetyl and 32 for 2,3-pentanedione. The results for each substrate were selected as the clu […]

library_books

A Computational Approach towards the Understanding of Plasmodium falciparum Multidrug Resistance Protein 1

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

[…] 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 and accessibilit […]

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

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