ArticleJournal of chemical theory and computation2022
PyLipID: A Python Package for Analysis of Protein-Lipid Interactions from Molecular Dynamics Simulations.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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105 citing papers in PubMed.
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- The SIMDA framework maps PIP2-binding sites regulating the KCNQ1 channel.Nature communications · 2026Article
- Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly.Nature communications · 2026Article
- Membrane Models and the Pursuit of Coherence.Biochemistry · 2026Review
- Transmembrane domain switching controls PINK1 import and fate in mitochondria.The EMBO journal · 2026Article
- The Shape of Things to Come: α-Helical Membrane Protein Folding on the Ribosome.Chemical reviews · 2026Review
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- Design principles of a membrane-spanning ubiquitin ligase.Molecular cell · 2026Article
- Molecular determinants of TNFR1:TNFα binding and dynamics in a physiological membrane environment.Current research in structural biology · 2026Article
- Cellular context and ligand class shape CXCR4-CCR5 heteromerization in live cells.Research square · 2026Article
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- Structural determinants for GPCR-mediated inhibition of TASK K2P channels by diacylglycerol and its dysfunction in disease.The EMBO journal · 2026Article
- Understanding cell-penetrating peptide mechanisms using computational electrophysiology simulations.Protein science : a publication of the Protein Society · 2026Article
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- Human class B1 GPCR modulation by plasma membrane lipids.Communications biology · 2026Article
- Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria.Nature communications · 2025Article
- The structure of the bacterial outer membrane transporter FusA enabled by addition of the native lipid lipopolysaccharide.Journal of structural biology: X · 2025Article
- MreB filaments in the elongasome modulate E. coli membrane curvature.Biophysical journal · 2025Article
45 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
Lipids play important modulatory and structural roles for membrane proteins. Molecular dynamics simulations are frequently used to provide insights into the nature of these protein-lipid interactions. Systematic comparative analysis requires tools that provide algorithms for objective assessment of such interactions. We introduce PyLipID, a Python package for the identification and characterization of specific lipid interactions and binding sites on membrane proteins from molecular dynamics simulations. PyLipID uses a community analysis approach for binding site detection, calculating lipid residence times for both the individual protein residues and the detected binding sites. To assist structural analysis, PyLipID produces representative bound lipid poses from simulation data, using a density-based scoring function. To estimate residue contacts robustly, PyLipID uses a dual-cutoff scheme to differentiate between lipid conformational rearrangements while bound from full dissociation events. In addition to the characterization of protein-lipid interactions, PyLipID is applicable to analysis of the interactions of membrane proteins with other ligands. By combining automated analysis, efficient algorithms, and open-source distribution, PyLipID facilitates the systematic analysis of lipid interactions from large simulation data sets of multiple species of membrane proteins.
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