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Materials-by-design: computation, synthesis, and characterization from atoms to structures

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Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers

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Optimizing Gō-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane

Mahmood, M. I., Poma, A. B., & Okazaki, K.-I. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.619381 · Cited by 42 · see citing works

Effective Molecular Dynamics from Neural Network-Based Structure Prediction Models

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Martinize2 and Vermouth: Unified Framework for Topology GenerationPreprint

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Efficient preparation and analysis of membrane and membrane protein systems

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Supramolecular Organization of Polymer Prodrug Nanoparticles Revealed by Coarse-Grained Simulations

Gao, P., Nicolas, J., & Ha‐Duong, T. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c05332 · Cited by 41 · see citing works

Synthetic Membrane Shaper for Controlled Liposome Deformation

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Complexation of single stranded RNA with an ionizable lipid: an all-atom molecular dynamics simulation study

Rissanou, A. N., Ouranidis, A., & Karatasos, K. (2020) · Soft Matter · doi:10.1039/d0sm00736f · Cited by 38 · see citing works

Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA

Assenza, S., & Pérez, R. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00138 · Cited by 39 · see citing works

Towards design of drugs and delivery systems with the Martini coarse-grained model

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pH‐Dependent Behavior of Ionizable Cationic Lipids in mRNA‐Carrying Lipoplexes Investigated by Molecular Dynamics Simulations

Settanni, G., Brill, W., Haas, H., & Schmid, F. (2021) · Macromolecular Rapid Communications · doi:10.1002/marc.202100683 · Cited by 38 · see citing works

Parameterization of Palmitoylated Cysteine, Farnesylated Cysteine, Geranylgeranylated Cysteine, and Myristoylated Glycine for the Martini Force Field

Atsmon‐Raz, Y., & Tieleman, D. P. (2017) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b10175 · Cited by 38 · see citing works

Molecular Dynamics Simulations in Drug Discovery and Drug Delivery

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Bottom-Up Coarse-Grained Modeling of DNA

Sun, T., Minhas, V., Korolev, N., Mirzoev, A., Lyubartsev, A. P., & Nordenskiöld, L. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.645527 · Cited by 38 · see citing works

Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies

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Peptide-DNA origami as a cryoprotectant for cell preservation

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Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes

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RNA origami: design, simulation and application

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MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing

Honorato, R. V., Roel‐Touris, J., & Bonvin, A. M. J. J. (2019) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2019.00102 · Cited by 33 · see citing works

Estimating the accuracy of the MARTINI model towards the investigation of peripheral protein–membrane interactions

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Developing a Coarse-Grained Model for Bacterial Cell Walls: Evaluating Mechanical Properties and Free Energy Barriers

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Improved Intracellular Delivery of Polyarginine Peptides with Cargoes

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In silico and in vitro design of cordycepin encapsulation in liposomes for colon cancer treatment

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Simulation of Complex Biomolecular Systems: The Ribosome Challenge

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Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery

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Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates

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Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

Dans, P. D., Gallego, D., Balaceanu, A., Darré, L., Gómez, H., & Orozco, M. (2018) · Chem · doi:10.1016/j.chempr.2018.09.015 · Cited by 33 · see citing works

A coarse-grained model for DNA origami

Reshetnikov, R. V., Stolyarova, A. V., Zalevsky, A. O., Panteleev, D. Y., Pavlova, G. V., Klinov, D. V., Golovin, A. V., & Protopopova, A. D. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1262 · Cited by 33 · see citing works

Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway

Jin, L., Tan, Y.-L., Wu, Y., Wang, X., Shi, Y.-Z., & Tan, Z.-J. (2019) · RNA · doi:10.1261/rna.071662.119 · Cited by 32 · see citing works

Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions

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Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses

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pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model

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Coarse-grained (hybrid) integrative modeling of biomolecular interactions

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Approaches and Perspective of Coarse-Grained Modeling and Simulation for Polymer–Nanoparticle Hybrid Systems

Khan, P. M., Kaushik, R., & Jayaraj, A. (2022) · ACS Omega · doi:10.1021/acsomega.2c06248 · Cited by 30 · see citing works

Assessing the Martini 3 protein model: A review of its path and potential

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Structure and conformational dynamics of scaffolded DNA origami nanoparticles

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Martinize2 and Vermouth: Unified Framework for Topology GenerationPreprint

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Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, Martini and oxDNA models

Naskar, S., & Maiti, P. K. (2021) · Journal of Materials Chemistry B · doi:10.1039/d0tb02970j · Cited by 29 · see citing works

Computational Nanoscopy of Tight Junctions at the Blood–Brain Barrier Interface

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Systematic Selection of High‐Affinity ssDNA Sequences to Carbon Nanotubes

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Martini 3 Building Blocks for Lipid Nanoparticle Design

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Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations

Ahmad, K., Javed, A., Lanphere, C., Coveney, P. V., Orlova, E. V., & Howorka, S. (2023) · Nature Communications · doi:10.1038/s41467-023-38681-5 · Cited by 26 · see citing works

Systematic coarse-grained modeling of complexation between small interfering RNA and polycations

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cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA

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ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field

Zhang, X., Sundram, S., Oppelstrup, T., Kokkila-Schumacher, S. I. L., Carpenter, T. S., Ingólfsson, H. I., Streitz, F. H., Lightstone, F. C., & Glosli, J. N. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0014500 · Cited by 25 · see citing works

Martini bead form factors for nucleic acids and their application in the refinement of protein–nucleic acid complexes against SAXS data

Paissoni, C., Jussupow, A., & Camilloni, C. (2019) · Journal of Applied Crystallography · doi:10.1107/s1600576719002450 · Cited by 25 · see citing works

Atomistic and coarse-grained simulations of membrane proteins: A practical guide

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Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments

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Development of transferable coarse-grained models of amino acids

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Driving forces of RNA condensation revealed through coarse-grained modeling with explicit Mg 2+

Li, S., & Chen, J. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2504583122 · Cited by 22 · see citing works

Adaptive resolution simulations of biomolecular systems

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Understanding the self-assembly and molecular structure of mRNA lipid nanoparticles at real size: Insights from the ultra-large-scale simulation

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Computer Aided Development of Nucleic Acid Applications in Nanotechnologies

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Temperature-Transferable Coarse-Grained Model for Poly(propylene oxide) to Study Thermo-Responsive Behavior of Triblock Copolymers

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Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding

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Recalibration of MARTINI-3 Parameters for Improved Interactions between Peripheral Proteins and Lipid Bilayers

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Dynamics of chromosome organization in a minimal bacterial cell

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Martini Coarse-Grained Force Field for RNA

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Coarse-grained RNA model for the Martini 3 force field

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Building RNA coarse-grained force fields: Design principles and training strategies

Li, W., & Chen, S. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.03.041 · Cited by 1 · see citing works

Covering All the Bases: A Martini Coarse-Grained Force Field for DNA

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One-bead coarse-grained model for RNA dynamics

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