HELIQUEST protocols

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HELIQUEST specifications

Information


Unique identifier OMICS_17721
Name HELIQUEST
Interface Web user interface
Restrictions to use None
Output data Text files or PDF
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Publication for HELIQUEST

HELIQUEST in pipelines

 (4)
2017
PMCID: 5266299
PMID: 28122029
DOI: 10.1371/journal.pone.0170821

[…] and molecular weights (mw) were predicted using the peptide property calculator from innovagen (http://pepcalc.com/ppc.php). schiffer-edmundson wheel representations of amps were obtained using heliquest [] from the expasy website (http://expasy.org/tools/). homologous amp sequences were obtained from the ncbi database and were aligned using clustalw (http://www.genome.jp/tools/clustalw/). […]

2017
PMCID: 5319999
PMID: 28275372
DOI: 10.3389/fmicb.2017.00273

[…] alignment of the obtained sequences of peptide ndbp-5.5 was performed using clustalw2 and bioedit software (). structural predictions, as shown in an alpha helix diagram, were generated by the heliquest server., molecular dynamics (md) simulations were performed with gromacs 5.1.3 (; ) using force field amber99sb-ildn () in order to explore the stability (or instability) of the peptide […]

2015
PMCID: 4467191
PMID: 25910939
DOI: 10.1242/bio.201410801

[…] pex11pγ were calculated using the emboss server (http://mobyle.pasteur.fr/cgi-bin/portal.py?form = hmoment). the helical wheel representation of the pex11p amphipathic region was prepared using the heliquest server (http://heliquest.ipmc.cnrs.fr)., liposomes were prepared essentially as described previously (). the lipid mixture was dried under nitrogen stream to form a thin lipid film, […]

2014
PMCID: 4020842
PMID: 24826994
DOI: 10.1371/journal.pone.0097539

[…] promoter primer., sequence analysis was carried out by using blastx (http://blast.ncbi.nlm.nih.gov/blast.cgi), dnaman, and genrunr. the secondary structure was analyzed by using the online program heliquest (http://heliquest.ipmc.cnrs.fr/cgi-bin/computparams.py) and measured by circular dichroism (cd) spectroscopy. the cd assay was performed at room temperature at the uv range of 190–250 nm […]


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HELIQUEST in publications

 (65)
PMCID: 5889406
PMID: 29626194
DOI: 10.1038/s41467-018-03717-8

[…] give the first and last amino acid in the protein sequence, with the total length of each protein given in bracketsb length is based on structural data, when available, and visual inspection using heliquest. prolines are considered as helix breakersc hydrophobic moment is calculated using heliquest. the ahs that contain 11-mer repeats are plotted as 3–11 helices. for longer ahs (*), the mean […]

PMCID: 5876494
PMID: 29628917
DOI: 10.3389/fmicb.2018.00541

[…] models were quantified by ramachandran plots using rampage (lovell et al., ) and by z-scores using prosa (wiederstein and sippl, ). the physiochemical parameters of the amps were predicted using heliquest (gautier et al., )., as dlp-ph was more effective against the growth of e. coli, we aimed to simulate the antimicrobial mechanism using the e. coli membrane model (pandit and klauda, ), […]

PMCID: 5852045
PMID: 29540735
DOI: 10.1038/s41598-018-22849-x

[…] the template., protein secondary structure and amphipathic α-helix prediction was done using amphipaseek v1.3.5 program as described,. helical-wheel projections of peptides were predicted using the heliquest server as described. cell lysates were collected by cell lysis in modified ripa lysis buffer (20 mm trishcl ph 7.4, 5 mm mgcl2, 100 mm nacl, 0.5% np-40 and 1x complete protease inhibitors) […]

PMCID: 5840792
PMID: 29510703
DOI: 10.1186/s12915-018-0492-9

[…] were likely present in the leca., mammalian gmap210 contains an n-terminal amphipathic alpha helix (alps domain), which is important for tethering er-derived vesicles to the cis-golgi []. using the heliquest web service [], we did not identify any such helices in the first 80 residues of gmap210 sequences from non-vertebrates, suggesting that this is a lineage-specific mechanism for recognition […]

PMCID: 5806080
PMID: 28594234
DOI: 10.1089/ars.2017.7164

[…] as proposed for the human prdx2 membrane interaction model (). protons or ca2+ ions may neutralize the negatively charged hydrophobic faces to imbed 2-cysprx in the membrane., the analysis with the heliquest program used the default settings. regions of at2-cysprx were selected with minimum 50% α-helical character, but no β-strand content and no dimer–dimer interaction site (). secondary […]


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HELIQUEST institution(s)
Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia Antipolis and CNRS, Valbonne, France
HELIQUEST funding source(s)
This work was supported by the Agence Nationale pour la Recherche and the CNRS (RISC).

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