ArticleJournal of chemical theory and computation2024
Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- GōMartini 3: From large conformational changes in proteins to environmental bias corrections.Nature communications · 2025Article
- Computational investigation of antiviral peptide interactions with Mpox DNA polymerase.In silico pharmacology · 2025Article
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3 authors.
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Abstract
Coarse-grained (CG) level molecular dynamics simulations are routinely used to study various biomolecular processes. The Martini force field is currently the most widely adopted parameter set for such simulations. The functional form of this and several other CG force fields enforces secondary protein structure support by employing a variety of harmonic potentials or restraints that favor the protein's native conformation. We propose a straightforward method to calculate the energetic consequences of transitions between predefined conformational states in systems in which multiple factors can affect protein conformational equilibria. This method is designed for use within the Martini force field and involves imposing conformational transitions by linking a Martini-inherent elastic network to the coupling parameter λ. We demonstrate the applicability of our method using the example of five biomolecular systems that undergo experimentally characterized conformational transitions between well-defined structures (
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