ArticleNature communications2025
Martini3-IDP: improved Martini 3 force field for disordered proteins.
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 36 papers.
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Who cites it
36 citing papers in PubMed.
- Article
- Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field.Journal of chemical information and modeling · 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
- Article
- A practical guide to investigating biomolecular condensates: a comment from the plant community.Science China. Life sciences · 2026Review
- Accurate interdomain contacts in a mixed folded protein from NMR-guided coarse-grained simulations.Physical chemistry chemical physics : PCCP · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- HyRes: Accurate Physics-Based Simulation of Dynamic Protein Structures and Interactions in Complex Environments at Scale.bioRxiv : the preprint server for biology · 2026Article
- Force-Induced Ankle Opening Reveals Mechanical Stabilization of the Ankle of Human β-Cardiac Myosin.ACS nano · 2026Article
- Fast Fourier Transform Enables Automated Parametrization of Complex Dihedral Potentials in All-Atom and Coarse-Grained Force Fields.Journal of chemical information and modeling · 2026Article
- An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies.Biophysical journal · 2026Article
- Sketching microprotein portraits.Protein science : a publication of the Protein Society · 2026Review
- Structuring Disorder via Supervised Molecular Dynamics: Uncovering Arginine-Glycine-Glycine-Mediated Ribonucleic Acid-Intrinsically Disordered Region Recognition Mechanisms.Journal of chemical information and modeling · 2026Article
- De novo design of peptides localizing at the interface of biomolecular condensates.Nature communications · 2026Article
- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
- Condensates as Conformation Editors of Disordered Client Proteins.Journal of the American Chemical Society · 2026Article
- Computational rheometry for modeling viscoelasticity and mechanical responses of biomolecular condensates.Biophysical journal · 2026Article
- Folded domains impose structural heterogeneity and attenuated dynamics in biomolecular condensates.Nature communications · 2026Article
- Physicochemical Principles Governing the Intrinsically Disordered Salivary Peptide Histatin 5: Ensemble Structure, Electrostatics, and Environmental Responsiveness.The journal of physical chemistry. B · 2026Review
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5 authors.
Funding
Abstract
Coarse-grained (CG) molecular dynamics (MD) is widely used for the efficient simulation of intrinsically disordered proteins (IDPs). The Martini model, one of the most popular CG force fields in biomolecular simulation, was reported to yield too compact IDP conformations, limiting its applications. Addressing this, we optimized the bonded parameters based on fitting to reference simulations of a diverse set of IDPs at atomistic resolution, resulting in a Martini3-based disordered protein model coined Martini3-IDP. This model leads to expanded IDP conformations, greatly improving the reproduction of the experimentally measured radii of gyration. Moreover, contrary to ad-hoc fixes based on scaling of protein-protein or protein-water interactions, Martini3-IDP keeps the overall interaction balance underlying Martini 3. To validate that, we perform a comprehensive testing including full-length multidomain proteins, IDP-lipid membrane binding and IDP-small molecule binding, confirming its ability to successfully capture the complex interplay between disordered proteins and diverse biomolecular components. Finally, the recently emerging concept of biomolecular condensate, through liquid-liquid phase separation, was also reproduced by Martini3-IDP for a number of both homotypic and heterotypic systems. With the improved Martini3-IDP model, we expand the ability to simulate processes involving IDPs in complex environments, at spatio-temporal scales inaccessible with all-atom models.
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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.