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MEMBPLUGIN specifications

Information


Unique identifier OMICS_12891
Name MEMBPLUGIN
Alternative name MEMBrane PLUGIN
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1
Stability Stable
Requirements
VMD
Maintained Yes

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Documentation


Maintainer


  • person_outline Toni Giorgino

Publication for MEMBrane PLUGIN

MEMBPLUGIN citations

 (16)
library_books

Structural insights into positive and negative allosteric regulation of a G protein coupled receptor through protein lipid interactions

2018
Sci Rep
PMCID: 5849739
PMID: 29535353
DOI: 10.1038/s41598-018-22735-6

[…] lipid phosphate group (centre-of-mass) was measured with PLUMED; (ii) membrane thickness calculated as average distance from lower to upper-leaflet phosphorus atoms, implementing default settings of MEMBPLUGIN within VMD over total simulation time; (iii) membrane density calculated across bilayer Z-axis using default settings of MEMBPLUGIN, analyzing mean mass of fatty acid chains and phosphate g […]

call_split

Molecular Mechanism of Resveratrol’s Lipid Membrane Protection

2018
Sci Rep
PMCID: 5785473
PMID: 29371621
DOI: 10.1038/s41598-017-18943-1
call_split See protocol

[…] at 1 atm and 310 K or 325 K, respectively. The analysis was performed using CPPTRAJ, R, and VMD program. Surface area per lipid, bilayer thickness and deuterium order parameters were calculated using MEMBPLUGIN 1.1. […]

library_books

Structure function relationships in ABCG2: insights from molecular dynamics simulations and molecular docking studies

2017
Sci Rep
PMCID: 5686161
PMID: 29138424
DOI: 10.1038/s41598-017-15452-z

[…] 5.0.7– was used for the MD simulations and protein insertion into the lipid membranes through the g_membed module. Areas per lipid (A L) and thickness (D HH) of all systems were calculated with the MembPlugin extension in VMD. Principal Component analysis (PCA) for the evaluation of the protein’s motion patterns was performed using the ProDy, software through the NMWiz plugin in VMD. Free energi […]

call_split

Proteoliposomal formulations of an HIV 1 gp41 based miniprotein elicit a lipid dependent immunodominant response overlapping the 2F5 binding motif

2017
Sci Rep
PMCID: 5234007
PMID: 28084464
DOI: 10.1038/srep40800
call_split See protocol

[…] in. Alignment was done using 3D-Coffee. The best of six models obtained from Modeller, as assessed by the DOPE (Discrete Optimized Protein Energy) method, was embedded in a POPC bilayer using the VMD membrane plugin, solvated with TIP3P water molecules (15 Å as minimal distance to the edge of the box). Additionally, Cl− and Na+ ions were added up to a final concentration of 0.15 M. The final struc […]

library_books

Gaussian Accelerated Molecular Dynamics in NAMD

2016
J Chem Theory Comput
PMCID: 5743237
PMID: 28034310
DOI: 10.1021/acs.jctc.6b00931

[…] DAJ) of the M3 receptor was used. After removal of TTP, the M3 receptor was inserted into a palmitoyl-oleoyl-phosphatidyl-choline (POPC) bilayer with all overlapping lipid molecules removed using the Membrane plugin and solvated in a water box using the Solvate plugin in VMD. Four ACh ligand molecules were placed at least 40 Å away from the receptor orthosteric site in the bulk solvent. The system […]

library_books

Structural and Functional Effect of an Oscillating Electric Field on the Dopamine D3 Receptor: A Molecular Dynamics Simulation Study

2016
PLoS One
PMCID: 5104473
PMID: 27832207
DOI: 10.1371/journal.pone.0166412

[…] riate orientation of the protein in the membrane was found by Server-Orientations of Proteins in Membranes (OPM) database.[] The 1-palmitoyl-2-oleoylsn-glycero-3- phosphatidylcholine (POPC) using the Membrane plugin distributed in VMD [] was used as a lipid bilayer which was equilibrated for at least 50 ns at T = 310 K and 1 atm within an NPT ensemble with anisotropic pressure coupling. D3R was or […]

Citations

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MEMBPLUGIN institution(s)
Pharmacoinformatics group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain; Department of Physics, Tampere University of Technology, Tampere, Finland; Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy
MEMBPLUGIN funding source(s)
Fundacio La Marato de TV3 (Ref.-No. 091010); Instituto de Salud Carlos III FEDER (CP12/03139); Alianza 4U program (JMRA); CNR’s short-term mobility (STM 2013) program

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