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Protocols

AmphipaSeek specifications

Information


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 No

Publication for AMPHIPATHIC IN-PLANE MEMBRANE ANCHORS PREDICTION

AmphipaSeek citations

 (14)
call_split

Membrane association of EMR2/ADGRE2 NTF is regulated by site specific N glycosylation

2018
Sci Rep
PMCID: 5852045
PMID: 29540735
DOI: 10.1038/s41598-018-22849-x
call_split See protocol

[…] 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 […]

library_books

Vacuolar protein sorting 13C is a novel lipid droplet protein that inhibits lipolysis in brown adipocytes

2017
PMCID: 5784322
PMID: 29175050
DOI: 10.1016/j.molmet.2017.10.014

[…] at 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), suggest […]

library_books

Oscillating behavior of Clostridium difficile Min proteins in Bacillus subtilis

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

[…] helical 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. B […]

library_books

The selective post translational processing of transcription factor Nrf1 yields distinct isoforms that dictate its ability to differentially regulate gene expression

2015
Sci Rep
PMCID: 4534795
PMID: 26268886
DOI: 10.1038/srep12983

[…] topology 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, […]

library_books

Sequence analysis reveals a conserved extension in the capping enzyme of the alphavirus supergroup, and a homologous domain in nodaviruses

2015
Biol Direct
PMCID: 4392871
PMID: 25886938
DOI: 10.1186/s13062-015-0050-0

[…] brome mosaic virus. Nevertheless, the potential amphipathic helix wihin αI in the alto group has strong support, since: 1) it is predicted by two programs relying on different methods, one of which, Amphipaseek, has very high specificity (above 95% []); 2) it is predicted in numerous taxa despite the lack of detectable sequence conservation, which seems to exclude a systematic bias in the softwar […]

library_books

Nucleoid occlusion protein Noc recruits DNA to the bacterial cell membrane

2015
PMCID: 4331003
PMID: 25568309
DOI: 10.15252/embj.201490177

[…] The CCCP sensitivity of MinD localisation was shown to be a result of the ΔΨ-stimulated membrane binding of its amphipathic helix (Strahl & Hamoen, ). Analysis of Noc using AMPHIPASEEK, a program designed to look for amphipathic in-plane membrane anchors (Sapay et al, ), highlighted a possible N-terminal amphipathic helix (Fig). A helical wheel projection of the N-termin […]


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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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