ArticleMolecular based mathematical biology2013
Progress in developing Poisson-Boltzmann equation solvers.
Article in Molecular based mathematical biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Testing a Heterogeneous Polarizable Continuum Model against Exact Poisson Boundary Conditions.Journal of chemical theory and computation · 2025Article
- Computational modeling of protein conformational changes - Application to the opening SARS-CoV-2 spike.Journal of computational physics · 2021Article
- A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation.Mathematical biosciences and engineering : MBE · 2020Article
- DelPhi Suite: New Developments and Review of Functionalities.Journal of computational chemistry · 2019Article
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.Journal of mathematical biology · 2019Article
- Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.Journal of computational chemistry · 2018Article
- Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations.Journal of chemical theory and computation · 2018Article
- Salt-bridge networks within globular and disordered proteins: characterizing trends for designable interactions.Journal of molecular modeling · 2017Article
- Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.Journal of computational chemistry · 2016Article
- Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.Scientific reports · 2016Article
- Synaptotagmin-1 binds to PIP(2)-containing membrane but not to SNAREs at physiological ionic strength.Nature structural & molecular biology · 2015Article
- Problems of robustness in Poisson-Boltzmann binding free energies.Journal of chemical theory and computation · 2015Article
- Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.Journal of computational chemistry · 2015Article
- On the energy components governing molecular recognition in the framework of continuum approaches.Frontiers in molecular biosciences · 2015Review
- Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi.Journal of computational chemistry · 2014Article
- On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function.Journal of theoretical & computational chemistry · 2014Article
Corrections and comments
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4 authors.
Funding
Abstract
This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects.
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