ArticleNature communications2025
GōMartini 3: From large conformational changes in proteins to environmental bias corrections.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Article
- Integrative structural modelling reveals the human Mic60-Mic19 subcomplex as a diffusion barrier in mitochondria.Nature communications · 2026Article
- Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field.Journal of chemical information and modeling · 2026Article
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- 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
- Molecular Mechanisms of KIT Receptor Dimerization and Oncogenic Activation Revealed by Multiscale Simulations.Journal of chemical information and modeling · 2026Article
- Ribosomal allostery as a potential regulator of bacterial dormancy.Nature communications · 2026Article
- Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics.Scientific reports · 2026Article
- Force-Induced Ankle Opening Reveals Mechanical Stabilization of the Ankle of Human β-Cardiac Myosin.ACS nano · 2026Article
- An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies.Biophysical journal · 2026Article
- Coarse-Grained Model of the Sodium Dodecyl Sulfate Anionic Surfactant Based on the MDPD-Martini Force Field.Langmuir : the ACS journal of surfaces and colloids · 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
- Martini 3 as a Transferable Force Field for Lipopolysaccharide Parametrization.The journal of physical chemistry. B · 2026Article
- Concentration Effects in Peptide-Lipid Bilayer Interactions: A Coarse-Grained Molecular Dynamics Study.The journal of physical chemistry. B · 2026Article
- Coarse-Grained Martini 3 Model of Chondroitin Sulfate A.Journal of chemical theory and computation · 2026Article
- Improving Conformational Ensembles of Folded Proteins in Go̅Martini.Journal of chemical theory and computation · 2026Article
- Oxygen depletion in biomolecular condensates is dominated by macromolecular density.Nature communications · 2026Article
- Coarse-grained Martini 3 model for collagen fibrils.Biophysical journal · 2026Article
- Recent advances in machine learning and coarse-grained potentials for biomolecular simulations.Biophysical journal · 2026Review
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access to spatio-temporal scales beyond all-atom based approaches. The GōMartini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency and accurate representation of protein dynamics with the capabilities of studying proteins in different biological environments. This paper introduces an enhanced GōMartini model, which combines a virtual-site implementation of Gō models with Martini 3. The implementation has been extensively tested by the community since the release of the reparametrized version of Martini. This work demonstrates the capabilities of the model in diverse case studies, ranging from protein-membrane binding to protein-ligand interactions and AFM force profile calculations. The model is also versatile, as it can address recent inaccuracies reported in the Martini protein model. Lastly, the paper discusses the advantages, limitations, and future perspectives of the Martini 3 protein model and its combination with Gō models.
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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.