ArticleBiophysical journal2010
Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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49 citing papers in PubMed.
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- The Effect of Arginine on the Phase Stability of Aqueous Hen Egg-White Lysozyme Solutions.International journal of molecular sciences · 2023Article
- Benchmarking Adaptive Steered Molecular Dynamics (ASMD) on CHARMM Force Fields.Chemphyschem : a European journal of chemical physics and physical chemistry · 2022Article
- Toward the solution of the protein structure prediction problem.The Journal of biological chemistry · 2021Review
- Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins.The journal of physical chemistry. B · 2020Article
- AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes.Nucleic acids research · 2020Article
- Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins.Biophysical journal · 2019Review
- Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties.The journal of physical chemistry letters · 2019Article
- Folding Molecular Dynamics Simulation of a gp41-Derived Peptide Reconcile Divergent Structure Determinations.ACS omega · 2018Article
- Developing a molecular dynamics force field for both folded and disordered protein states.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes.The journal of physical chemistry. B · 2017Article
- Studying the role of cooperative hydration in stabilizing folded protein states.Journal of structural biology · 2016Article
- The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate.Journal of the American Chemical Society · 2016Article
- Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data.Protein science : a publication of the Protein Society · 2016Article
- Advances in free-energy-based simulations of protein folding and ligand binding.Current opinion in structural biology · 2016Review
- Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment.Scientific reports · 2016Article
- Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.Protein science : a publication of the Protein Society · 2016Article
- Accelerated molecular dynamics simulations of protein folding.Journal of computational chemistry · 2015Article
- Current status of protein force fields for molecular dynamics simulations.Methods in molecular biology (Clifton, N.J.) · 2015Article
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2 authors.
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Abstract
The ability to fold proteins on a computer has highlighted the fact that existing force fields tend to be biased toward a particular type of secondary structure. Consequently, force fields for folding simulations are often chosen according to the native structure, implying that they are not truly "transferable." Here we show that, while the AMBER ff03 potential is known to favor helical structures, a simple correction to the backbone potential (ff03( *)) results in an unbiased energy function. We take as examples the 35-residue alpha-helical Villin HP35 and 37 residue beta-sheet Pin WW domains, which had not previously been folded with the same force field. Starting from unfolded configurations, simulations of both proteins in Amber ff03( *) in explicit solvent fold to within 2.0 A RMSD of the experimental structures. This demonstrates that a simple backbone correction results in a more transferable force field, an important requirement if simulations are to be used to interpret folding mechanism.
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