{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T06:27:18Z","timestamp":1781245638171,"version":"3.54.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: 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\u2013lipid 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.<\/jats:p><jats:p>Availability and implementation: MEMBPLUGIN is a VMD extension written in Tcl. Multi-platform source code, documentation and tutorials are freely available at http:\/\/membplugin.sourceforge.net.<\/jats:p><jats:p>Contact: \u00a0toni.giorgino@isib.cnr.it or jana.selent@upf.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu037","type":"journal-article","created":{"date-parts":[[2014,1,23]],"date-time":"2014-01-23T01:47:51Z","timestamp":1390441671000},"page":"1478-1480","source":"Crossref","is-referenced-by-count":298,"title":["MEMBPLUGIN: studying membrane complexity in VMD"],"prefix":"10.1093","volume":"30","author":[{"given":"Ramon","family":"Guix\u00e0-Gonz\u00e1lez","sequence":"first","affiliation":[{"name":"1 Pharmacoinformatics group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, 2Department of Physics, Tampere University of Technology, Tampere, Finland and 3Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ismael","family":"Rodriguez-Espigares","sequence":"additional","affiliation":[{"name":"1 Pharmacoinformatics group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, 2Department of Physics, Tampere University of Technology, Tampere, Finland and 3Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan Manuel","family":"Ram\u00edrez-Anguita","sequence":"additional","affiliation":[{"name":"1 Pharmacoinformatics group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, 2Department of Physics, Tampere University of Technology, Tampere, Finland and 3Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pau","family":"Carri\u00f3-Gaspar","sequence":"additional","affiliation":[{"name":"1 Pharmacoinformatics group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, 2Department of Physics, Tampere University of Technology, Tampere, Finland and 3Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hector","family":"Martinez-Seara","sequence":"additional","affiliation":[{"name":"1 Pharmacoinformatics group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, 2Department of Physics, Tampere University of Technology, Tampere, Finland and 3Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toni","family":"Giorgino","sequence":"additional","affiliation":[{"name":"1 Pharmacoinformatics group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, 2Department of Physics, Tampere University of Technology, Tampere, Finland and 3Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"Selent","sequence":"additional","affiliation":[{"name":"1 Pharmacoinformatics group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, 2Department of Physics, Tampere University of Technology, Tampere, Finland and 3Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,1,21]]},"reference":[{"key":"2023041302465411900_","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1145\/235815.235821","article-title":"The quickhull algorithm for convex hulls","volume":"22","author":"Barber","year":"1996","journal-title":"ACM Trans. Math. Softw."},{"key":"2023041302465411900_","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/nchembio.1338","article-title":"A distinct mechanism for activating uncoupled nicotinic acetylcholine receptors","volume":"9","author":"daCosta","year":"2013","journal-title":"Nat. Chem. Biol."},{"key":"2023041302465411900_","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.2119\/molmed.2011.00119","article-title":"Severe alterations in lipid composition of frontal cortex lipid rafts from Parkinson\u2019s disease and incidental Parkinson\u2019s disease","volume":"17","author":"Fabelo","year":"2011","journal-title":"Mol. Med."},{"key":"2023041302465411900_","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. 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