ArticleThe journal of physical chemistry. B2017
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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Who cites it
97 citing papers in PubMed.
- Training a force field for proteins and small molecules from scratch.Chemical science · 2026Article
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- Orally Bioavailable and Site-Selective Covalent STING Inhibitor Derived from a Macrocyclic Marine Diterpenoid.Journal of medicinal chemistry · 2025Article
- Ligand recognition by 14-3-3 proteins requires negative charges but not necessarily phosphorylation.FEBS letters · 2025Article
- Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.Journal of chemical information and modeling · 2025Article
- HydE Catalytic Mechanism Is Powered by a Radical Relay with Redox-Active Fe(I)-Containing Intermediates.Journal of the American Chemical Society · 2025Article
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- Negative Charges, Not Necessary Phosphorylation, are Required for Ligand Recognition by 14-3-3 Proteins.bioRxiv : the preprint server for biology · 2024Article
- Predicting binding events in very flexible, allosteric, multi-domain proteins.bioRxiv : the preprint server for biology · 2024Article
- Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields.The journal of physical chemistry. B · 2024Article
- Machine-learned molecular mechanics force fields from large-scale quantum chemical data.Chemical science · 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
- System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields.Journal of chemical theory and computation · 2024Article
- Tuning Potential Functions to Host-Guest Binding Data.Journal of chemical theory and computation · 2024Article
- Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data.Communications chemistry · 2023Article
- Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering.Biomacromolecules · 2023Article
- Enzymatic β-elimination in natural product O- and C-glycoside deglycosylation.Nature communications · 2023Article
37 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.
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