ArticleeLife2025
Martinize2 and Vermouth provide a unified framework for molecular topology generation.
Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 137 papers.
What it found
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Who cites it
137 citing papers in PubMed.
- Self-assembly of sodium caprate in simulated intestinal fluids and with a therapeutic peptide: A small-angle neutron scattering study.International journal of pharmaceutics: X · 2026Article
- Full-length SARS-CoV-2 envelope protein adopts an interfacial topology in lipid bilayers.Biochimica et biophysica acta. Biomembranes · 2026Article
- Presynaptic accumulation of APP-CTFβ may contribute to synaptic dysfunction in Alzheimer's disease.The EMBO journal · 2026Article
- Article
- Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field.Journal of chemical information and modeling · 2026Article
- Lipidomic Profile Reconstruction of Therapeutic Membrane Targets Using Physics-Based Optimization with Limited Activity Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Structural and functional basis of antinociceptive action of χ-conotoxin AoIA at the noradrenaline transporter.Nature structural & molecular biology · 2026Article
- The molecular basis of mitochondrial crista formation by the MIC10 complex.Science advances · 2026Article
- Amphipathic β‑Sheet-Forming Octapeptide Self-Assembly Using the Martini Potential Family.ACS omega · 2026Article
- Integrating AI and Molecular Modeling for Structural Prediction of a Closed-Pore State of the hERG Channel.Journal of chemical information and modeling · 2026Article
- Comparing multislice projections of MD simulations with cryo-EM exposes structural prediction errors.Biophysical journal · 2026Article
- The Sec11 C-terminal short helix promotes productive engagement of internal signal sequences with the signal peptidase complex.The Journal of biological chemistry · 2026Article
- MartiniSurf: Automated Simulations of Surface-Immobilized Biomolecular Systems with Martini.Journal of chemical information and modeling · 2026Article
- Article
- Kinesin-5/Cut7 C-terminal tail phosphorylation influence on motor regulation through multi-scale molecular modeling.Biophysical journal · 2026Article
- Polymer Molecular Weight Influences Cancer Cell Surface Retention and Cytokine Presentation by Layer-by-Layer Nanoparticles.ACS nano · 2026Article
- Accurate interdomain contacts in a mixed folded protein from NMR-guided coarse-grained simulations.Physical chemistry chemical physics : PCCP · 2026Article
- Temperature-Dependent Menthol Binding across TRPM8 Conformational States.Journal of the American Chemical Society · 2026Article
- Molecular Mechanisms of KIT Receptor Dimerization and Oncogenic Activation Revealed by Multiscale Simulations.Journal of chemical information and modeling · 2026Article
- Simulations show increased lipid interdigitation in transmembrane coupling of protein condensates.bioRxiv : the preprint server for biology · 2026Article
77 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design by high-throughput (HT) simulations is another forefront of MD. In these areas, the Martini coarse-grained force field, especially the latest version (i.e. v3), is being actively explored because it offers an enhanced spatial-temporal resolution. However, the automation tools for preparing simulations with the Martini force field, accompanying the previous version, were not designed for HT simulations or studies of complex cellular systems. Therefore, they become a major limiting factor. To address these shortcomings, we present the open-source
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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.