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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 in publications

 (12)
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 […]

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 […]

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 […]

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 […]

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 […]

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

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