ArticleJournal of chemical theory and computation2021
Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane-Water Partitioning.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- SMartini: automated small molecule parametrization for Martini 3 force field.bioRxiv : the preprint server for biology · 2026Article
- Martini Mapper: An Automated Fragment-Based Mapping Algorithm for Developing Coarse-Grained Models within the Martini 3 Framework.Journal of chemical information and modeling · 2026Article
- Automated parametrization of small molecules within the Martini 3 coarse-grained model guided by experimental log P values.Scientific reports · 2025Article
- Polyimide Polymer Simulations through Coarse-Grained Modeling: Prediction of Structure, Physical Properties, and Gas Separation Properties.The journal of physical chemistry. B · 2025Article
- Toward the Evolutionary Optimisation of Small Molecules Within Coarse-Grained Simulations: Training Molecules to Hide Behind Lipid Head Groups.The journal of physical chemistry. B · 2025Article
- Molecular Dynamics Simulations Reveal Octanoylated Hyaluronic Acid Enhances Liposome Stability, Stealth and Targeting.ACS omega · 2024Article
- Leveraging Machine Learning-Guided Molecular Simulations Coupled with Experimental Data to Decipher Membrane Binding Mechanisms of Aminosterols.Journal of chemical theory and computation · 2024Article
- Self-Assembly of Lamellae-in-Lamellae by Double-Tail Cationic Surfactants.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization.Journal of chemical theory and computation · 2023Article
- Automatic identification of chemical moieties.Physical chemistry chemical physics : PCCP · 2023Article
- Direct Modulators of K-Ras-Membrane Interactions.ACS chemical biology · 2023Article
- Molecular dynamics simulation of an entire cell.Frontiers in chemistry · 2023Article
- Antibody-nanobody combination increases their neutralizing activity against SARS-CoV-2 and nanobody H11-H4 is effective against Alpha, Kappa and Delta variants.Scientific reports · 2022Article
- Current State and Perspectives of Simulation and Modeling of Aliphatic Isocyanates and Polyisocyanates.Polymers · 2022Review
- Towards design of drugs and delivery systems with the Martini coarse-grained model.QRB discovery · 2022Review
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With a view to high-throughput simulations, we present an automated system for mapping and parameterizing organic molecules for use with the coarse-grained Martini force field. The method scales to larger molecules and a broader chemical space than existing schemes. The core of the mapping process is a graph-based analysis of the molecule's bonding network, which has the advantages of being fast, general, and preserving symmetry. The parameterization process pays special attention to coarse-grained beads in aromatic rings. It also includes a method for building efficient and stable frameworks of constraints for molecules with structural rigidity. The performance of the method is tested on a diverse set of 87 neutral organic molecules and the ability of the resulting models to capture octanol-water and membrane-water partition coefficients. In the latter case, we introduce an adaptive method for extracting partition coefficients from free-energy profiles to take into account the interfacial region of the membrane. We also use the models to probe the response of membrane-water partitioning to the cholesterol content of the membrane.
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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 OpenQuestion graph.