ArticleJournal of computational chemistry2017
Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria.
Article in Journal of computational chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed.
- Mechanistic studies on HNRNPA2B1 suggest binding but not selective recognition of mRNA biology · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.Journal of chemical theory and computation · 2026Article
- RBM45 Preferential Binding to mThe journal of physical chemistry. B · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.ArXiv · 2026Article
- Likely Overstabilization of Charge-Charge Interactions in CHARMM36m(w): A Case for a99SB-disp Water.The journal of physical chemistry. B · 2024Article
- Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.Journal of chemical theory and computation · 2024Article
- Article
- Replica exchange molecular dynamics simulations reveal self-association sites in M-crystallin caused by mutations provide insights of cataract.Scientific reports · 2021Article
- When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes.Biomolecules · 2021Review
- Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.Biomolecules · 2021Review
- Cancer-Associated Mutations Perturb the Disordered Ensemble and Interactions of the Intrinsically Disordered p53 Transactivation Domain.Journal of molecular biology · 2021Article
- Identification of an α-MoRF in the Intrinsically Disordered Region of the Escargot Transcription Factor.ACS omega · 2020Article
- Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins.Biophysical journal · 2020Article
- Targeting Intrinsically Disordered Proteins through Dynamic Interactions.Biomolecules · 2020Review
- Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units.Journal of computational chemistry · 2020Article
- Article
- Residual Structures and Transient Long-Range Interactions of p53 Transactivation Domain: Assessment of Explicit Solvent Protein Force Fields.Journal of chemical theory and computation · 2019Article
- Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins.Biomolecules · 2019Review
- Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.Journal of chemical theory and computation · 2019Article
- Atomistic Peptide Folding Simulations Reveal Interplay of Entropy and Long-Range Interactions in Folding Cooperativity.Scientific reports · 2018Article
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2 authors.
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Abstract
Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors. The latter has been hampered by the difficulty of generating converged conformational ensembles of non-trivial model proteins using the popular replica exchange sampling technique. Here, we leverage improved sampling efficiency of a newly developed multi-scale enhanced sampling technique to re-optimize the generalized-Born with molecular volume (GBMV2) implicit solvent model with the CHARMM36 protein force field. Recursive optimization of key GBMV2 parameters (such as input radii) and protein torsion profiles (via the CMAP torsion cross terms) has led to a more balanced GBMV2 protein force field that recapitulates the structures and stabilities of both helical and β-hairpin model peptides. Importantly, this force field appears to be free of the over-compaction bias, and can generate structural ensembles of several intrinsically disordered proteins of various lengths that seem highly consistent with available experimental data. © 2017 Wiley Periodicals, Inc.
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