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Volarea specifications

Information


Unique identifier OMICS_08148
Name Volarea
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Maria J. Ramos

Publication for Volarea

Volarea citations

 (4)
library_books

Helical unwinding and side chain unlocking unravel the outward open conformation of the melibiose transporter

2016
Sci Rep
PMCID: 5034317
PMID: 27658476
DOI: 10.1038/srep33776

[…] cγ of y33 (extracellular end of tm1) and y256 (extracellular end of tm7), compared to the initial state (post-equilibration), and (ii) the water occupancy in the periplasmic cavity measured using volarea (). this double criteria approach allowed us to discriminate between replicas simply increasing its inner cavity pore radius compared to replicas opening towards the periplasmic side. […]

library_books

Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis

2016
Sci Rep
PMCID: 4757871
PMID: 26887338
DOI: 10.1038/srep21763

[…] studies can profile the dimerization and allosteric regulation mechanism of mglu1. as shown in , the occupied surface areas of ligand fitm and six cholesterol molecules on mglu1 are calculated by volarea. the cholesterol molecules occupy an area about 450 å2 in dimer a or b during the molecular dynamics simulations. it indicates that the cholesterol molecules can interact with dimer a and b. […]

library_books

Ultrastable cellulosome adhesion complex tightens under load

2014
Nat Commun
PMCID: 4266597
PMID: 25482395
DOI: 10.1038/ncomms6635

[…] between acceptor and hydrogen should be <3.5 å; second, the angle between hydrogen-donor-acceptor should be <30°. surface contact areas of interacting residues were calculated employing volarea implemented in vmd. the area is calculated using a probe radius defined as an in silico rolling spherical probe that is screened around the area of doc exposed to coh and also coh area […]

library_books

ANGDelMut – a web based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis associated angiogenin mutations

2014
F1000Res
PMCID: 3901456
PMID: 24555108
DOI: 10.5256/f1000research.2772.r2228

[…] to examine the ribonucleolytic activity. the nuclear translocation activity of the submitted ang mutant is examined by calculating the sasa of nuclear localization signal residues 31rrr 33 using volarea ( http://www2.fc.up.pt/portobiocomp/software/volarea/home.html), a vmd plug-in., step 4: data output. the output panel shows whether the user-submitted ang mutation exhibited conformational […]


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Volarea institution(s)
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal

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