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GalaxySite specifications

Information


Unique identifier OMICS_03792
Name GalaxySite
Interface Web user interface
Restrictions to use None
Input data A protein sequence or a protein structure.
Input format FASTA, PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Chaok Seok
  • person_outline GalaxyRefine Team
  • person_outline Myeong Sup Lee

Publication for GalaxySite

GalaxySite citations

 (4)
library_books

Molecular and Structural Characterization of the Tegumental 20.6 kDa Protein in Clonorchis sinensis as a Potential Druggable Target

2017
Int J Mol Sci
PMCID: 5372573
PMID: 28273846
DOI: 10.3390/ijms18030557

[…] COACH [] was used to predict calcium-binding sites in the N-terminal region of CsTegu20.6, based on the identification of analogs with similar binding sites. GalaxySite [] was employed to predict specifically binding non-metal ligands and their binding conformations for screening putative inhibitors of CsTegu20.6. The detailed information regarding specifi […]

library_books

Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

2015
Int J Mol Sci
PMCID: 4691145
PMID: 26694353
DOI: 10.3390/ijms161226202

[…] nergetic methods (SITEHOUND [], VISCANA [], SiteComp [], and FTMap []); 3. Miscellaneous methods, which use information from homology or template-based modelling (FunFOLD3 [,], COACH [], COFACTOR [], GalaxySite [], GASS [], VISM-CFA [], and PLIP []), Surface accessibility based methods such as LigSiteCSC [], in addition to Physicochemical properties exploited by Andersson and colleagues []. Exampl […]

library_books

Modeling enzyme ligand binding in drug discovery

2015
J Cheminform
PMCID: 4594084
PMID: 26457119
DOI: 10.1186/s13321-015-0096-0

[…] tructure where their binding conformation is optimized using the LigDockCSA protein–ligand docking program []. Binding-site residues are then identified based on their proximity to the docked ligand. GalaxySite was extensively tested on different ligand binding prediction test sets, on which it showed superior or similar performance compared to other state of the art prediction methods.Moreover, S […]

library_books

Structure Based Computational Study of Two Disease Resistance Gene Homologues (Hm1 and Hm2) in Maize (Zea mays L.) with Implications in Plant Pathogen Interactions

2014
PLoS One
PMCID: 4029905
PMID: 24847713
DOI: 10.1371/journal.pone.0097852

[…] The active site pockets of the modeled HCTRs were predicted using CASTp server . In addition, GalaxySite tool of GalaxyWEB server was employed to predict the ligand and cofactor binding sites. Further, COFACTOR tool (an award-winning method for function prediction in the community-wide CASP9 […]

Citations

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GalaxySite institution(s)
Department of Chemistry, Seoul National University, Seoul, Korea; Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, Korea
GalaxySite funding source(s)
Supported by National Research Foundation of Korea (2013R1A2A1A09012229, 2012M3C1A6035362 and 2013R1A1A2058447) and Asan Institute for Life Sciences, Seoul, Korea (2013–591 and 2014-607).

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