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Citations per year

Number of citations per year for the bioinformatics software tool iMembrane
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This map represents all the scientific publications referring to iMembrane per scientific context
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Protocols

iMembrane specifications

Information


Unique identifier OMICS_14316
Name iMembrane
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A membrane protein sequence or structure.
Output data The predicted membrane insertion of the input protein, the query and match structure visualization, the sequence alignment visualization, a list of all generated models and some links to view or download these, the results list showing all the hits for a query in a tabular format.
License Other
Computer skills Basic
Stability Stable
Requirements
JavaScript, Java, Sun Java
Maintained Yes

Documentation


Maintainer


  • person_outline Sebastian Kelm

Publication for iMembrane

iMembrane citations

 (6)
library_books

A model for studying the energetics of sustained high frequency firing

2018
PLoS One
PMCID: 5927439
PMID: 29708986
DOI: 10.1371/journal.pone.0196508

[…] ds strongly on large amplitude stimuli in this way seems ill-suited for Eigenmannia’s robust high frequency EOD output.The MKZ model assumes an isopotential electrocyte in which the membrane current (Imembrane) charges and discharges 50 nF of membrane capacitance. While space-clamp (isopotential) is necessary for electrocyte voltage clamp recordings, electrocytes are in general not isopotential in […]

library_books

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

2017
Comput Struct Biotechnol J
PMCID: 5312651
PMID: 28228927
DOI: 10.1016/j.csbj.2017.01.008

[…] n sequence to a structural template, requiring the identification of one or more homologs that the structure is based on (e.g. PROSPECT , RAPTOR , pGenTHREADER , pro-sp3-TASSER , MODELER , I-TASSER , iMembrane ), (ii) the third involves the use of simulated annealing algorithms, which are based on the general principles that govern protein structure and energetics and therefore does not require a […]

call_split

Examining the Conservation of Kinks in Alpha Helices

2016
PLoS One
PMCID: 4912094
PMID: 27314675
DOI: 10.1371/journal.pone.0157553
call_split See protocol

[…] til they satisfied the criteria for a helical seed used by MC-HELAN []. For membrane proteins, helices were only kept if at least one residue was annotated to be in the tail region of the membrane by iMembrane [].An all-against-all structural comparison of the protein chains in a set was carried out, using TM-align []. Pairs of helices were considered homologous if: the number of residues in the l […]

library_books

Helix kinks are equally prevalent in soluble and membrane proteins

2014
Proteins
PMCID: 4285789
PMID: 24638929
DOI: 10.1002/prot.24550

[…] inates were removed. These proteins were split into their constituent chains, and filtered using the same criteria as for the soluble data set. The membrane position for each residue was annotated by iMembrane, with only chains annotated with ≥1 residue in the tail region of the membrane retained. All remaining non membrane proteins were removed by visual inspection. Only 20 chains had resolution […]

library_books

The Role of Diatom Nanostructures in Biasing Diffusion to Improve Uptake in a Patchy Nutrient Environment

2013
PLoS One
PMCID: 3646848
PMID: 23667421
DOI: 10.1371/journal.pone.0059548

[…] s I = 2DsC, where D is molecular diffusivity, s is the opening radius and C is the background concentration . For comparing the diffusion to the membrane versus to the bulk water we took the ratio of Imembrane/Ibulk, which becomes Idifference = smembrane/sbulk. For Coscinodiscus sp., the areolae opening radius is 575 nm and the sieve plate opening radius to the bulk water is 22 nm. There are 50 sm […]

library_books

A cationic lumen in the Wzx flippase mediates anionic O antigen subunit translocation in Pseudomonas aeruginosa PA01

2012
Mol Microbiol
PMCID: 3412221
PMID: 22554073
DOI: 10.1111/j.1365-2958.2012.08084.x

[…] ivity of a given truncation set to obtain normalized activity ratios (NAR) (). NAR for the PhoALacZα fusions under investigation were displayed on a segmented model of WzxPa overlaid with output from iMembrane (), a program that predicts the position of a membrane protein within a lipid bilayer based on molecular dynamics simulations (). NAR of < 0.01, 0.01–100 and > 100 are representative of cyto […]


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iMembrane institution(s)
Department of Statistics, University of Oxford, Oxford, UK; UCB Celltech, Branch of UCB Pharma SA, Slough, UK
iMembrane funding source(s)
Biotechnology and Biological Sciences Research Council and University of Oxford Systems Biology Doctoral Training Centre.

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