ArticleJournal of chemical information and modeling2023
Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Comparative molecular dynamics of two cyclic peptide inhibitors bound to the Zika virus NS2B/NS3 protease.Journal of molecular modeling · 2026Article
- K16F/E22F Mutation Promotes Oligomerization and Alters β-Sheet Topology of Aβ16-22 Peptides: Insights from Molecular Dynamics Simulations.ACS chemical neuroscience · 2026Article
- Peptide-based drug design using generative AI.Chemical communications (Cambridge, England) · 2026Review
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Dual-Locking the SARS-CoV-2 Spike Trimer: An Amphipathic Molecular "Bolt" Stabilizes Conserved Druggable Interfaces for Coronavirus Inhibition.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations.Computational and structural biotechnology journal · 2025Article
- In Silico Modeling and Characterization of Epstein-Barr Virus Latent Membrane Protein 1 Protein.ACS omega · 2024Article
- Modeling protein motions through reinforcement learning.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Energy Landscapes and Structural Ensembles of Glucagon-like Peptide-1 Monomers.The journal of physical chemistry. B · 2024Article
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4 authors.
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Abstract
Accelerated molecular dynamics (aMD) protocols were assessed on predicting the secondary structure of eight peptides, of which two are helical, three are β-hairpins, and three are disordered. Protocols consisted of combinations of three force fields (ff99SB, ff14SB, ff19SB) and two explicit solvation models (TIP3P and OPC), and were evaluated in two independent aMD simulations, one starting from an extended conformation, the other starting from a misfolded conformation. The results of these analyses indicate that all three combinations performed well on helical peptides. As for β-hairpins, ff19SB performed well with both solvation methods, with a slight preference for the TIP3P solvation model, even though performance was dependent on both peptide sequence and initial conformation. The ff19SB/OPC combination had the best performance on intrinsically disordered peptides. In general, ff14SB/TIP3P suffered the strongest helical bias.
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