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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 in publications

 (6)
PMCID: 5928576
PMID: 29712573
DOI: 10.1186/s12915-018-0514-7

[…] \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \delta ratio=\frac{icytoplasm{t}_x}{imembrane{t}_x}-\frac{icytoplasm{t}_0}{imembrane{t}_0} $$\end{document}δratio=icytoplasmtximembranetx-icytoplasmt0imembranet0where tx refers to the time point after light irradiation and t0 […]

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

[…] 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 […]

PMCID: 4912094
PMID: 27314675
DOI: 10.1371/journal.pone.0157553

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]

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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