ArticleJournal of chemical information and modeling2025
MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- The physicochemical design, structure and permeability of the JCVI-syn3A minimal cell membrane.Nature communications · 2026Article
- Amphipathic β‑Sheet-Forming Octapeptide Self-Assembly Using the Martini Potential Family.ACS omega · 2026Article
- Martini 3 Metabolome.Journal of chemical theory and computation · 2026Article
- Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution across Different Lipid Environments.Biomacromolecules · 2026Article
- Effects of Liposome Composition and Size on Protein Corona Formation: Competitive Replacement of Abundant Proteins by High-Affinity Proteins on the Liposome Surface.Advanced healthcare materials · 2026Article
- Ultrasound-responsive liposomes: A mechanistic framework to decode the effects of acoustic parameters.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Probiotic Potential, Genomic Characterization, and In Silico Insights of FiveAntibiotics (Basel, Switzerland) · 2026Article
- Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution Across Different Lipid Environments.bioRxiv : the preprint server for biology · 2026Article
- Oxygen depletion in biomolecular condensates is dominated by macromolecular density.Nature communications · 2026Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As molecular modeling gains ever more prominence in understanding cellular processes, high quality visualization of models and dynamics has never been more important. Naturally, much molecular visualization software is written to enable the visualization of atomic level details in structures. While necessary, this means that visualization of increasingly popular coarse-grained (CG) models remains a challenge. Here, we present a Python package, MartiniGlass, that facilitates the visualization of systems simulated with the widely used CG Martini force field using the popular visualization package VMD. MartiniGlass rapidly processes molecular topologies and accounts for important topological features at CG resolution, such as secondary structure restraints, preparing them for easy visualization of simulated trajectories.
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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 Socratic graph.