ArticleChemical physics letters2013
Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.
Article in Chemical physics letters, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Extending MMPBSA for membrane proteins: Addressing P2YBiophysical journal · 2026Article
- Article
- Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations.Journal of computer-aided molecular design · 2023Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation.Mathematical biosciences and engineering : MBE · 2020Article
- Improved Poisson-Boltzmann Methods for High-Performance Computing.Journal of chemical theory and computation · 2019Article
- DelPhi Suite: New Developments and Review of Functionalities.Journal of computational chemistry · 2019Article
- Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies.Journal of chemical information and modeling · 2019Article
- An efficient second-order poisson-boltzmann method.Journal of computational chemistry · 2019Article
- Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units.Journal of chemical information and modeling · 2019Article
- Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling.The journal of physical chemistry. B · 2017Article
- Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units.Journal of chemical theory and computation · 2017Article
- A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins.Journal of chemical theory and computation · 2017Article
- Numerical interpretation of molecular surface field in dielectric modeling of solvation.Journal of computational chemistry · 2017Article
- DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.Journal of computational chemistry · 2017Article
- Recent Developments and Applications of the MMPBSA Method.Frontiers in molecular biosciences · 2017Review
- Modeling Membrane Protein-Ligand Binding Interactions: The Human Purinergic Platelet Receptor.The journal of physical chemistry. B · 2016Article
- Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis.Journal of computational chemistry · 2016Article
- Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions.The journal of physical chemistry. B · 2016Article
- Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation.Journal of chemical information and modeling · 2015Article
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6 authors.
Funding
Abstract
Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.
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