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Protocols

HexServer specifications

Information


Unique identifier OMICS_03776
Name HexServer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for HexServer

HexServer citations

 (12)
library_books

Mechanism of Apoptosis Induction by Mycoplasmal Nuclease MGA_0676 in Chicken Embryo Fibroblasts

2018
PMCID: 5893762
PMID: 29670864
DOI: 10.3389/fcimb.2018.00105

[…] 2 (http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi) and homology remodeling tools (http://swissmodel.expasy.org/workspace/index). Prediction of the interactions between proteins was done using the Hexserver tool (http://hexserver.loria.fr/). Software programs, such as DNAstar, DNAMAN, and Primer Premier 5, were also used in the analyses. […]

library_books

Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures

2017
Int J Mol Sci
PMCID: 5751226
PMID: 29206185
DOI: 10.3390/ijms18122623

[…] thus makes the calculations 8.8 times faster than ZDOCK. The method is set up to perform massive numbers of calculations that are run on parallel computing systems, and along with GPU.proton.DOCK and HexServer demonstrates the increase in search speed when using hardware acceleration.FRODOCK projects the interaction terms of a potential protein complex into 3D grid-based potentials using spherical […]

library_books

Movement Protein of Cucumber Mosaic Virus Associates with Apoplastic Ascorbate Oxidase

2016
PLoS One
PMCID: 5036820
PMID: 27668429
DOI: 10.1371/journal.pone.0163320

[…] tp://zhanglab.ccmb.med.umich.edu/I-TASSER/). The quality of the 3D-model of MP was evaluated using PROCHECK tool at SAVS server (http://nihserver.mbi.ucla.edu/SAVES/). Docking was performed using the HexServer (http://hexserver.loria.fr.). CsAO4 and MP were uploaded as inputs into Hex and treated as receptor and ligand, respectively. Molecular interactions between proteins were predicted using Lig […]

library_books

Screening for protein protein interactions using Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM)

2016
Sci Rep
PMCID: 4919659
PMID: 27339025
DOI: 10.1038/srep28186

[…] Docking programs Hex (http://hexserver.loria.fr/index.php) and ClusPro (http://nrc.bu.edu/cluster) were used for rigid body docking and to run simulations of the heterodimers consisting of the monomer structures of MST1 (PDB: 2JO […]

library_books

Novel Immunomodulatory Flagellin Like Protein FlaC in Campylobacter jejuni and Other Campylobacterales

2015
PMCID: 4863622
PMID: 27303676
DOI: 10.1128/mSphere.00028-15

[…] htly bound to the affinity beads in the absence of FlaC. Modeling the structure of the TLR5-FlaC heterotetramer according to the recently published TLR5 ectodomain crystal structure () using HexDock (HexServer) () proposed a thermodynamically favorable interaction interface between the two proteins, specifically at the FlaC D1 domain (). The modeled TLR5-FlaC heterotetramer arrangement has similar […]

call_split

α Mangostin Disrupts the Development of Streptococcus mutans Biofilms and Facilitates Its Mechanical Removal

2014
PLoS One
PMCID: 4211880
PMID: 25350668
DOI: 10.1371/journal.pone.0111312
call_split See protocol

[…] n (http://www.ncbi.nlm.nih.gov/pccompound). MarvinSketch software was utilized for obtaining the α-mangostin structure in a PDB format (http://www.chemaxon.com/products/marvin/marvinsketch/), and the HexServer (HEX 6.9 software) was accessed for calculating and displaying protein-ligand docking (http://hexserver.loria.fr/). The parameters used for docking included: Correlation type (Shape only), F […]

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HexServer institution(s)
Department of Computing Science, Lillybank Gardens, University of Glasgow, Scotland, UK

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