ArticleJournal of chemical information and modeling2022
Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 37 citations in OpenAlex.
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- Characterization of Membrane Binding and Protein-Lipid Interactions at the Atomic Level with an Accelerated HMMM Model.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1).Nature communications · 2025Article
- AlphaFold-Guided Bespoke Gene Editing Enhances Field-Grown Soybean Oil Contents.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
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- Tumor-acquired somatic mutation affects conformation to abolish ABCG2-mediated drug resistance.Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy · 2024Article
- Functional regulation of aquaporin dynamics by lipid bilayer composition.Nature communications · 2024Article
- Integrative analysis of pathogenic variants in glucose-6-phosphatase based on an AlphaFold2 model.PNAS nexus · 2024Article
- Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter.Nature communications · 2023Article
- Ionizable Amino Lipids Distribution and Effects on DSPC/Cholesterol Membranes: Implications for Lipid Nanoparticle Structure.The journal of physical chemistry. B · 2023Article
- Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition.bioRxiv : the preprint server for biology · 2023Article
- Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Structural Elucidation of Ivermectin Binding to α7nAChR and the Induced Channel Desensitization.ACS chemical neuroscience · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Molecular dynamics (MD) simulations of biological membranes have achieved such levels of sophistication that are commonly used to predict unresolved structures and various properties of lipids and to substantiate experimental data. While achieving sufficient sampling of lipid dynamics remains a major challenge, a commonly used method to improve lipid sampling, e.g., in terms of specific interactions with membrane-associated proteins, is to randomize the initial arrangement of lipid constituents in multiple replicas of simulations, without changing the overall lipid composition of the membrane of interest. Here, we introduce a method that can rapidly generate multiple replicas of lipid bilayers with different spatial and conformational configurations for any given lipid composition. The underlying algorithm, which allows one to shuffle lipids at any desired level, relies on the application of an external potential, here referred to as the "carving potential", that removes clashes/entanglements before lipid positions are exchanged (shuffled), thereby minimizing the energy penalty due to abrupt lipid repositioning. The method is implemented as "Membrane Mixer Plugin (MMP) 1.0" in VMD, with a convenient graphical user interface that guides the user in setting various options and parameters. The plugin is fully automated and generates new membrane replicas more rapidly and conveniently than other analogous tools. The plugin and its capabilities introduced here can be extended to include additional features in future versions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.