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Epock specifications

Information


Unique identifier OMICS_06810
Name Epock
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Epock

Epock in publications

 (5)
PMCID: 5847559
PMID: 29560272
DOI: 10.1038/s41421-018-0009-2

[…] 2 μs of simulation. to monitor volume of the cytoplasmic pocket over the course of simulation, trajectories were aligned based on backbone atoms of tm1–7 using mdtraj 1.7.2 and analyzed using the epock command line tool. the cytoplasmic pocket was defined by an include_sphere (r = 9.0 å) slightly below the “npxxy” tyrosine hydroxyl group and a contigous_sphere (r = 5.0 å) placed […]

PMCID: 5667471
PMID: 29096714
DOI: 10.1186/s13287-017-0705-0

[…] by quantification of mineral content by the cetylpyridinium chloride (cpc) extraction method, as described previously []. optical density (od) was measured at 550 nm using a microplate reader (epock; biotek instruments, inc., vt, usa)., all experiments were run in two to four replicates and repeated at least three times. statistical analysis of the data employed one-way or two-way analysis […]

PMCID: 5620967
PMID: 28979936
DOI: 10.1021/acscentsci.7b00211

[…] and molecular surfaces and probes (e.g., hole, surfnet). other algorithms analyze ensembles of structures, but usually require a preliminary structural alignment (e.g., mdpocket, pocketanalizerpca, epock, trj_cavity, and trapp). in this case, the resulting information may depend on the specific reference structure used for the alignment. atom-based algorithms (e.g., provar and eposbp) avoid […]

PMCID: 5298994
PMID: 28232803
DOI: 10.3389/fphys.2017.00038

[…] energy function. the top scored model for each protein was selected for further analysis., pore radius profiles for our molecular models and the template crystal structure were computed with the epock cavity detector plugin (laurent et al., ), as implemented in vmd (humphrey et al., ). to do so, a prospective axis of 120 and 200å in length for hcs and gjcs, respectively, was traced along […]

PMCID: 5145807
PMID: 27866853
DOI: 10.1016/j.str.2016.10.005

[…] the channel and to the conductance of the channel when open (). a number of related tools for analysis and display of channels and pores in channels have also since been developed; e.g., mole () and epock (). however, these methods are generally based on the physical dimensions of pores and cavities within proteins, and do not include explicit calculations of the likelihood of water and/or ions […]

Epock institution(s)
Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France; Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, UK

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