ArticleJournal of chemical theory and computation2022
Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.Journal of chemical theory and computation · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.ArXiv · 2026Article
- PEGASUS: Unlocking Polarity in Cell-Permeable Cyclic Peptides Using AI Models Built on Massively Parallel Biological Assays.Journal of medicinal chemistry · 2026Article
- Molecular Design in l-Glutamic Acid-Based Peptide Assembly Dynamics Driven by Carbodiimide-Fueled Reaction Cycle.Biomacromolecules · 2026Article
- Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints.Journal of chemical theory and computation · 2025Article
- Review
- A general graph neural network based implicit solvation model for organic molecules in water.Chemical science · 2024Article
- Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.Journal of chemical theory and computation · 2024Article
- Exploring Structural Insights of Aβ42 and α-Synuclein Monomers and Heterodimer: A Comparative Study Using Implicit and Explicit Solvent Simulations.The journal of physical chemistry. B · 2024Article
- Effects of Charge Sequence Pattern and Lysine-to-Arginine Substitution on the Structural Stability of Bioinspired Polyampholytes.Biomacromolecules · 2024Article
- Article
- Differentiable simulation to develop molecular dynamics force fields for disordered proteins.Chemical science · 2024Article
- Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes.Journal of chemical information and modeling · 2024Article
- Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans.Journal of chemical information and modeling · 2023Article
- Uncovering the Contributions of Charge Regulation to the Stability of Single Alpha Helices.Chemphyschem : a European journal of chemical physics and physical chemistry · 2023Article
- Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations.RSC advances · 2023Article
- Simulation Reveals the Chameleonic Behavior of Macrocycles.Journal of chemical information and modeling · 2023Article
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Authors and funding
4 authors.
Funding
Abstract
We test a range of standard generalized Born (GB) models and protein force fields for a set of five experimentally characterized, designed peptides comprising alternating blocks of glutamate and lysine, which have been shown to differ significantly in α-helical content. Sixty-five combinations of force fields and GB models are evaluated in >800 μs of molecular dynamics simulations. GB models generally do not reproduce the experimentally observed α-helical content, and none perform well for all five peptides. These results illustrate that these models are not usefully predictive in this context. These peptides provide a useful test set for simulation methods.
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