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APL@voro—interactive visualization and analysis of cell membrane simulations
SUMMARY: Molecular dynamics (MD) simulations of cell membranes allow for a better understanding of complex processes such as changing membrane dynamics, lipid rafts and the incorporation/passing of macromolecules into/through membranes. To explore and understand cell membrane compositions, dynamics...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9969824/ https://www.ncbi.nlm.nih.gov/pubmed/36752505 http://dx.doi.org/10.1093/bioinformatics/btad083 |
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author | Kern, Martin Jaeger-Honz, Sabrina Schreiber, Falk Sommer, Bjorn |
author_facet | Kern, Martin Jaeger-Honz, Sabrina Schreiber, Falk Sommer, Bjorn |
author_sort | Kern, Martin |
collection | PubMed |
description | SUMMARY: Molecular dynamics (MD) simulations of cell membranes allow for a better understanding of complex processes such as changing membrane dynamics, lipid rafts and the incorporation/passing of macromolecules into/through membranes. To explore and understand cell membrane compositions, dynamics and processes, visual analytics can help to interpret MD simulation data. APL@Voro is a software for the interactive visualization and analysis of cell membrane simulations. Here, we present the new APL@Voro, which has been continuously developed since its initial release in 2013. We discuss newly implemented algorithms, methodologies and features, such as the interactive comparison of related simulations and methods to assign lipids to either the upper or lower leaflet. AVAILABILITY AND IMPLEMENTATION: The current open-source version of APL@Voro can be downloaded from http://aplvoro.com. |
format | Online Article Text |
id | pubmed-9969824 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-99698242023-02-28 APL@voro—interactive visualization and analysis of cell membrane simulations Kern, Martin Jaeger-Honz, Sabrina Schreiber, Falk Sommer, Bjorn Bioinformatics Applications Note SUMMARY: Molecular dynamics (MD) simulations of cell membranes allow for a better understanding of complex processes such as changing membrane dynamics, lipid rafts and the incorporation/passing of macromolecules into/through membranes. To explore and understand cell membrane compositions, dynamics and processes, visual analytics can help to interpret MD simulation data. APL@Voro is a software for the interactive visualization and analysis of cell membrane simulations. Here, we present the new APL@Voro, which has been continuously developed since its initial release in 2013. We discuss newly implemented algorithms, methodologies and features, such as the interactive comparison of related simulations and methods to assign lipids to either the upper or lower leaflet. AVAILABILITY AND IMPLEMENTATION: The current open-source version of APL@Voro can be downloaded from http://aplvoro.com. Oxford University Press 2023-02-08 /pmc/articles/PMC9969824/ /pubmed/36752505 http://dx.doi.org/10.1093/bioinformatics/btad083 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Kern, Martin Jaeger-Honz, Sabrina Schreiber, Falk Sommer, Bjorn APL@voro—interactive visualization and analysis of cell membrane simulations |
title | APL@voro—interactive visualization and analysis of cell membrane simulations |
title_full | APL@voro—interactive visualization and analysis of cell membrane simulations |
title_fullStr | APL@voro—interactive visualization and analysis of cell membrane simulations |
title_full_unstemmed | APL@voro—interactive visualization and analysis of cell membrane simulations |
title_short | APL@voro—interactive visualization and analysis of cell membrane simulations |
title_sort | apl@voro—interactive visualization and analysis of cell membrane simulations |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9969824/ https://www.ncbi.nlm.nih.gov/pubmed/36752505 http://dx.doi.org/10.1093/bioinformatics/btad083 |
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