MEMBPLUGIN: studying membrane complexity in VMD.
CONCLUSIONS
Computer simulations are giving way to more complex and accurate studies of biological membranes by molecular dynamics (MD) simulations. The analysis of MD trajectories comprises the biophysical characterization of membrane properties or the study of protein-lipid interactions and dynamics. However, there is a lack of automated tools to analyse MD simulations of complex membrane or membrane-protein systems. Here we present MEMBPLUGIN, a plugin for the Visual Molecular Dynamics package that provides algorithms to measure a host of essential biophysical properties in simulated membranes. MEMBPLUGIN features are accessible both through a user-friendly graphical interface and as command-line procedures to be invoked in analysis scripts.


METHODS
MEMBPLUGIN is a VMD extension written in Tcl. Multi-platform source code, documentation and tutorials are freely available at http://membplugin.sourceforge.net.


BACKGROUND
toni.giorgino@isib.cnr.it or jana.selent@upf.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
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 and Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy.
Ramon
R
Guixà-González
Ismael
I
Rodriguez-Espigares
Juan Manuel
JM
Ramírez-Anguita
Pau
P
Carrió-Gaspar
Hector
H
Martinez-Seara
Toni
T
Giorgino
Jana
J
Selent
D000465:Algorithms; D008563:Membrane Lipids / Q000032:analysis / Q000378:metabolism; D008565:Membrane Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D011381:Programming Languages; D017434:Protein Structure, Tertiary
D008563:Membrane Lipids; D008565:Membrane Proteins