ArticleJournal of chemical theory and computation2021
Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20.
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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15 citing papers in PubMed.
- Molecular dynamics study on surface adsorption of hexyl trimethylammonium bromide, octyl trimethylammonium bromide, sodium hexyl sulfate, and sodium heptyl sulfate.Journal of molecular modeling · 2026Article
- Fractional Ion Contributions to Mixed Electrolyte Ion Atmospheres from Experimental Thermodynamic Data.The journal of physical chemistry. B · 2026Article
- Quantifying ion-ion association in mixed electrolyte systems using bulk thermodynamic experimental data.The Journal of chemical physics · 2026Article
- Ion Adsorption at Surfaces from Local and Global Electroneutrality Constraints.Langmuir : the ACS journal of surfaces and colloids · 2026Article
- Spatially anion-confined electrolyte enables high-rate and durable anode-free sodium batteries.Science advances · 2026Article
- Article
- Hydration Contribution to the Solvation Free Energy of Water-Soluble Polymers.The journal of physical chemistry. B · 2025Article
- Ion-Ion Association in Bulk Mixed Electrolytes Using Global and Local Electroneutrality Constraints.The journal of physical chemistry. B · 2025Article
- The intrinsically disordered transcriptional activation domain of CIITA is functionally tuneable by single substitutions: An exception or a new paradigm?Protein science : a publication of the Protein Society · 2024Article
- Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes.Biophysical chemistry · 2024Article
- Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein.The Journal of chemical physics · 2023Article
- Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties.Journal of chemical theory and computation · 2022Article
- Protein assembly and crowding simulations.Current opinion in structural biology · 2022Review
- Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory.International journal of molecular sciences · 2021Review
- Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Applications of KBFF20.Journal of chemical theory and computation · 2021Article
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Authors and funding
12 authors.
Funding
Abstract
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.
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