ArticleJournal of chemical theory and computation2013
Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 52 citations in OpenAlex.
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- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.ArXiv · 2026Article
- Implicit Solvent Models and Their Applications in Biophysics.Biomolecules · 2025Review
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Differentiable simulation to develop molecular dynamics force fields for disordered proteins.Chemical science · 2024Article
- The design of functional proteins using tensorized energy calculations.Cell reports methods · 2023Article
- A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model.The Journal of chemical physics · 2023Article
- Theoretical and Data-Driven Approaches for Biomolecular Condensates.Chemical reviews · 2023Review
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Unifying coarse-grained force fields for folded and disordered proteins.Current opinion in structural biology · 2022Review
- Mechanism of negative membrane curvature generation by I-BAR domains.Structure (London, England : 1993) · 2021Article
- When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes.Biomolecules · 2021Review
- Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods.Frontiers in molecular biosciences · 2021Article
- Identification of an α-MoRF in the Intrinsically Disordered Region of the Escargot Transcription Factor.ACS omega · 2020Article
- Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model.The journal of physical chemistry. B · 2018Article
- Looking at the Disordered Proteins through the Computational Microscope.ACS central science · 2018Review
- Membrane Curvature Sensing by Amphipathic Helices: Insights from Implicit Membrane Modeling.Biophysical journal · 2018Article
- Protein structure refinement using a quantum mechanics-based chemical shielding predictor.Chemical science · 2017Article
- Correction to Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data.Journal of chemical theory and computation · 2017Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 3 institutions in 4 countries.
Funding
Abstract
The development of accurate implicit solvation models with low computational cost is essential for addressing many large-scale biophysical problems. Here, we present an efficient solvation term based on a Gaussian solvent-exclusion model (EEF1) for simulations of proteins in aqueous environment, with the primary aim of having a good overlap with explicit solvent simulations, particularly for unfolded and disordered states - as would be needed for multiscale applications. In order to achieve this, we have used a recently proposed coarse-graining procedure based on minimization of an entropy-related objective function to train the model to reproduce the equilibrium distribution obtained from explicit water simulations. Via this methodology, we have optimized both a charge screening parameter and a backbone torsion term against explicit solvent simulations of an
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.