ArticleNature communications2023
LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria.Nature communications · 2025Article
- Combining Cryo-EM with Computational Approaches To Revolutionize Structural Biology.The protein journal · 2025Review
- Research progress on TMEM proteins in cancer progression and chemoresistance (Review).International journal of molecular medicine · 2025Review
- Membrane Composition Modulates Vp54 Binding: A Combined Experimental and Computational Study.Pathogens (Basel, Switzerland) · 2025Article
- Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales.Current opinion in structural biology · 2025Review
- Machine learning techniques for lipid nanoparticle formulation.Nano convergence · 2025Review
- Assembly and the gating mechanism of the Pel exopolysaccharide export complex PelBC of Pseudomonas aeruginosa.Nature communications · 2025Article
- MprF fromScience advances · 2025Article
- The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations.Journal of molecular biology · 2025Review
- Mapping structural and dynamic divergence across the MBOAT family.Structure (London, England : 1993) · 2024Article
- Three-Dimensional Interaction Homology: Deconstructing Residue-Residue and Residue-Lipid Interactions in Membrane Proteins.Molecules (Basel, Switzerland) · 2024Article
- Lipid regulation of the glucagon receptor family.The Journal of endocrinology · 2024Review
- LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.Nature communications · 2023Article
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Authors and funding
13 authors.
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Abstract
Cryo-electron microscopy (cryo-EM) enables the determination of membrane protein structures in native-like environments. Characterising how membrane proteins interact with the surrounding membrane lipid environment is assisted by resolution of lipid-like densities visible in cryo-EM maps. Nevertheless, establishing the molecular identity of putative lipid and/or detergent densities remains challenging. Here we present LipIDens, a pipeline for molecular dynamics (MD) simulation-assisted interpretation of lipid and lipid-like densities in cryo-EM structures. The pipeline integrates the implementation and analysis of multi-scale MD simulations for identification, ranking and refinement of lipid binding poses which superpose onto cryo-EM map densities. Thus, LipIDens enables direct integration of experimental and computational structural approaches to facilitate the interpretation of lipid-like cryo-EM densities and to reveal the molecular identities of protein-lipid interactions within a bilayer environment. We demonstrate this by application of our open-source LipIDens code to ten diverse membrane protein structures which exhibit lipid-like densities.
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