AmphipaSeek protocols

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AmphipaSeek specifications

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Unique identifier OMICS_17720
Name AmphipaSeek
Alternative name AMPHIPATHIC IN-PLANE MEMBRANE ANCHORS PREDICTION
Interface Web user interface
Restrictions to use None
Programming languages C, Python
Computer skills Basic
Stability Stable
Maintained Yes

Publication for AMPHIPATHIC IN-PLANE MEMBRANE ANCHORS PREDICTION

AmphipaSeek in pipeline

2016
PMCID: 4905992
PMID: 26817670
DOI: 10.1002/mbo3.337

[…] str. k‐12 substr. mg1655; taxid: 511145). specific strains of clostridia were selected based on the availability of their whole genome sequence. the positions amphipatic helices were predicted using amphipaseek (sapay et al. ). multiple alignment of protein sequences was done using clustalw plugin of clc sequence viewer 7.6 software (clc bio, cambridge, ma)., our first question to address […]


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AmphipaSeek in publications

 (14)
PMCID: 5852045
PMID: 29540735
DOI: 10.1038/s41598-018-22849-x

[…] (l333d, l341e and l344e) in ah was generated in a two-step pcr procedure by using ah-egfp cdna as 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 […]

PMCID: 5784322
PMID: 29175050
DOI: 10.1016/j.molmet.2017.10.014

[…] vps13c is abundantly expressed in bat and it concentrates on lds., proteins binding lds directly contain α-amphipathic helix or hydrophobic hairpin domains. analysis of vps13c protein sequence using amphipaseek , identified two regions around amino acids 2550 and 3535 with high amphipathic score that were predicted to be inserted in the membrane parallel to the membrane plane (in-plane), […]

PMCID: 4905992
PMID: 26817670
DOI: 10.1002/mbo3.337

[…] region that anchors it to the membrane (szeto et al. ). this consensus sequence can also be found in c.difficile mind (fig. b) and an amphipathic helix was also predicted at the c‐terminus by amphipaseek (not shown; sapay et al. ). this helix would then be responsible for the membrane localization of mindcd in b.subtilis, which is similar to that observed for mindec in the same organism., […]

PMCID: 4534795
PMID: 26268886
DOI: 10.1038/srep12983

[…] of nrf1 was predicted using several bioinformatic algorithms, including the toppred (http://mobyle. pasteur.fr/cgi-bin/portal.py?form=toppred), heliquest (http://heliquest.ipmc.cnrs.fr/) and amphipaseek (http://npsa-pbil.ibcp. fr/cgi-bin/npsa_automat.pl?page=/npsa/npsa_amphipaseek.html) programmes. the pest sequence, as a potential proteolytic cleavage site for proteasome and/or calpain, […]

PMCID: 4392871
PMID: 25886938
DOI: 10.1186/s13062-015-0050-0

[…]  ) [,]. these amphipathic helices are doubly underlined in additional file : figure s2.figure 4, we searched for other potential membrane-binding, amphipathic helices in the alto mtase-gtase by using amphipaseek [] and refining its predictions with heliquest [] (see ). the amphipathic helices predicted by amphipaseek are thickly underlined in additional file : figure s2, and their sequence and loc […]


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AmphipaSeek institution(s)
Institut de Biologie et Chimie des Protéines, CNRS-Univ. Lyon 1 – IFR128 BioSciences Lyon-Gerland, Lyon, France; LORIA-CNRS, Campus Scientifique, Vandœuvre-lès-Nancy, France

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