ArticlePhysical chemistry chemical physics : PCCP2008
Assessing the performance of implicit solvation models at a nucleic acid surface.
Article in Physical chemistry chemical physics : PCCP, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Connecting Gas-Phase Computational Chemistry to Condensed Phase Kinetic Modeling: The State-of-the-Art.Polymers · 2021Review
- 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
- Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling.The journal of physical chemistry. B · 2017Article
- Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.The journal of physical chemistry. B · 2013Article
- Variational approach for nonpolar solvation analysis.The Journal of chemical physics · 2012Article
- Differential geometry based solvation model II: Lagrangian formulation.Journal of mathematical biology · 2011Article
- Differential geometry based solvation model I: Eulerian formulation.Journal of computational physics · 2010Article
- The AGBNP2 Implicit Solvation Model.Journal of chemical theory and computation · 2009Article
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Authors and funding
3 authors.
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Abstract
Implicit solvation models are popular alternatives to explicit solvent methods due to their ability to "pre-average" solvent behavior and thus reduce the need for computationally-expensive sampling. Previously, we have demonstrated that Poisson-Boltzmann models for polar solvation and integral-based models for nonpolar solvation can reproduce explicit solvation forces in a low-charge density protein system. In the present work, we examine the ability of these continuum models to describe solvation forces at the surface of a RNA hairpin. While these models do not completely describe all of the details of solvent behavior at this highly-charged biomolecular interface, they do provide a reasonable description of average solvation forces and therefore show significant promise for developing more robust implicit descriptions of solvent around nucleic acid systems for use in biomolecular simulation and modeling. Additionally, we observe fairly good transferability in the nonpolar model parameters optimized for protein systems, suggesting its robustness for modeling general nonpolar solvation phenomena in biomolecular systems.
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