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PoreWalker specifications

Information


Unique identifier OMICS_04691
Name PoreWalker
Interface Web user interface
Restrictions to use None
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Marialuisa Pellegrini-Calace

Publication for PoreWalker

PoreWalker citations

 (12)
library_books

Diversity of Nicotinic Acetylcholine Receptor Positive Allosteric Modulators Revealed by Mutagenesis and a Revised Structural Model

2018
PMCID: 5767682
PMID: 29196491
DOI: 10.1124/mol.117.110551

[…] addition, comparison between the open and closed conformations revealed a concerted movement of all four helices in the tm domain. analysis of the channel lumen of the two α7 structural models with porewalker (european bioinformatics institute, wellcome genome campus, uk) () revealed a dilation between the closed and open α7 comparative models (supplemental fig. 3)., to identify potential […]

library_books

Outer membrane phospholipase A’s roles in Helicobacter pylori acid adaptation

2017
PMCID: 5469174
PMID: 28616083
DOI: 10.1186/s13099-017-0184-y

[…] using what if (as implemented in the yasara/what if twinset), where solvent exclusion maps were produced for spherical probes with radius p using the surface map option in what if (srfmap) [, ]. porewalker was used to estimate possible pore paths (see fig.  in additional file ) []., , electronic supplementary material , the online version of this article […]

library_books

Genome wide identification, characterization, and expression profile of aquaporin gene family in flax (Linum usitatissimum)

2017
Sci Rep
PMCID: 5406838
PMID: 28447607
DOI: 10.1038/srep46137

[…] form hourglass like structure with six transmembrane domains (see ). pore structure and three dimensional geometry of a channel of tip3 (tip3–1, tip3–2, tip3–3, tip3–4) family members obtained with “porewalker” software identified a pore that longitudinally runs from the extracellular to intracellular opening of the protein. the pore morphology clearly showed conservation of pore size and two […]

library_books

Observation of σ pore currents in mutant hKv1.2_V370C potassium channels

2017
PLoS One
PMCID: 5398642
PMID: 28426823
DOI: 10.1371/journal.pone.0176078

[…] we modelled the σ-pore in hkv1.2_v370c similar to what was described for the hkv1.3_v388c mutant channel [] i.e. using the caver program, visualizing the pore with pymol® and verifying it with porewalker as shown in . for the hkv1.2_v370c mutant channel the entry of the σ-pore is located on the extracellular side of the channel between y377 (shaker position 445) on the back surface […]

library_books

Altered Channel Conductance States and Gating of GABAA Receptors by a Pore Mutation Linked to Dravet Syndrome

2017
eNeuro
PMCID: 5301078
PMID: 28197552
DOI: 10.1523/ENEURO.0251-16.2017

[…] detection and pore shape and visualization of the 3d structural models of the wt and mutated (p302l) gabaa receptor in the open, closed, and desensitized conformation states were determined using porewalker (), a computational automated method available as a web-based resource (http://www.ebi.ac.uk/thornton-srv/software/porewalker/). from the porewalker outputs, a list of the identified […]

library_books

Soybean TIP Gene Family Analysis and Characterization of GmTIP1;5 and GmTIP2;5 Water Transport Activity

2016
Front Plant Sci
PMCID: 5073556
PMID: 27818669
DOI: 10.3389/fpls.2016.01564

[…] for both gmtip5;1 and gmtip5;2., tertiary protein structure predicted for tips showed six conserved transmembrane domains. however, the three dimensional geometry of the pore structure obtained with porewalker software () showed substantial variation in pore size and constrictions in the pore. the tertiary structure and pore morphology for gmtip1;5 and gmtip2;5 are shown in figure ., […]


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PoreWalker institution(s)
EMBL/EBI, The Wellcome Trust Genome Campus, Cambridge, UK

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