ArticleProceedings of the National Academy of Sciences of the United States of America2003
Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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81 citing papers in PubMed.
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- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA.Journal of chemical theory and computation · 2024Article
- Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains.The journal of physical chemistry. B · 2024Article
- Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment.Journal of chemical theory and computation · 2024Article
- Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks.ACS central science · 2023Article
- Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks.bioRxiv : the preprint server for biology · 2023Article
- Structure-Thermodynamic Relationship of a Polysaccharide Gel (Alginate) as a Function of Water Content and Counterion Type (Na vs Ca).The journal of physical chemistry. B · 2023Article
- Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations.RSC advances · 2023Article
- RLDOCK method for predicting RNA-small molecule binding modes.Methods (San Diego, Calif.) · 2022Article
- RLDOCK: A New Method for Predicting RNA-Ligand Interactions.Journal of chemical theory and computation · 2020Article
- Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.Journal of chemical theory and computation · 2020Article
- Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies.Journal of chemical theory and computation · 2018Article
- Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.Journal of chemical information and modeling · 2017Article
- Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber.Journal of chemical theory and computation · 2016Article
- Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations.Journal of chemical theory and computation · 2016Article
- Folding and Stabilization of Native-Sequence-Reversed Proteins.Scientific reports · 2016Article
- Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.Journal of chemical theory and computation · 2015Article
- Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations.Biophysical journal · 2015Article
21 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
We compare simulations using the generalized Born/surface area (GB/SA) implicit solvent model with simulations using explicit solvent (transferable intermolecular potential 3 point, TIP3P) to test the GB/SA algorithm. We use the replica exchange molecular dynamics method to sample the conformational phase space of two alpha-helical peptides, A21 and the Fs, by using two different classical potentials and both water models. We find that when using GB/SA: (i) A21 is predicted to be more helical than the Fs peptide at all temperatures; (ii) the native structure of the Fs peptide is predicted to be a helical bundle instead of a single helix; and (iii) the persistence length and most probable end-to-end distance are too large in the unfolded state when compared against the explicit solvent simulations. We find that the potential of mean force in the phi(psi) plane is markedly different in the two solvents, making the two simulated peptides respond differently when the backbone torsions are perturbed. A fit of the temperature melting curves obtained in these simulations to a Lifson-Roig model finds that the GB/SA model has an unphysically large nucleation parameter, whereas the explicit solvent model produces values similar to experiment.
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