ArticleThe Journal of chemical physics2018
Explicit ions/implicit water generalized Born model for nucleic acids.
Article in The Journal of chemical physics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- RLDOCKScore: A Scoring Function for RNA-Ligand Docking and Small Molecule Virtual Screening.Journal of chemical theory and computation · 2025Article
- Structure and Zeta Potential of Gold Nanoparticles with Coronas of Varying Size and Composition.The journal of physical chemistry. C, Nanomaterials and interfaces · 2025Article
- Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA.Journal of chemical theory and computation · 2024Article
- Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.Journal of chemical information and modeling · 2024Article
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Uncovering water effects in protein-ligand recognition: importance in the second hydration shell and binding kinetics.Physical chemistry chemical physics : PCCP · 2023Article
- Graph deep learning locates magnesium ions in RNA.QRB discovery · 2022Article
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor: Application to Spermine Synthase Enzyme.Frontiers in molecular biosciences · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes-disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na
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Registered trials
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.