ArticleJournal of chemical theory and computation2010
A revised density function for molecular surface definition in continuum solvent models.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Grid-Context Convolutional Model for Efficient Molecular Surface Construction from Point Clouds.Journal of chemical theory and computation · 2025Article
- Calculation of solvation force in molecular dynamics simulation by deep-learning method.Biophysical journal · 2024Article
- Grid-Robust Efficient Neural Interface Model for Universal Molecule Surface Construction from Point Clouds.The journal of physical chemistry letters · 2023Article
- Article
- Exploring the druggability of the binding site of aurovertin, an exogenous allosteric inhibitor of FFrontiers in pharmacology · 2022Article
- Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations.Journal of chemical theory and computation · 2021Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- Improved Poisson-Boltzmann Methods for High-Performance Computing.Journal of chemical theory and computation · 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
- Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid.The Journal of chemical physics · 2017Article
- A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins.Journal of chemical theory and computation · 2017Article
- Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units.Journal of chemical theory and computation · 2017Article
- Numerical interpretation of molecular surface field in dielectric modeling of solvation.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
- Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design.PLoS computational biology · 2016Article
- Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion.Journal of molecular biology · 2016Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
A revised density function is developed to define the molecular surface for the numerical Poisson-Boltzmann methods to achieve a better convergence and higher numerical stability. The new density function does not use any predefined functional form but is numerically optimized to reproduce the reaction field energies computed with the solvent excluded surface definition. An exhaustive search in the parameter space is utilized in the optimization using a wide-range training molecules including proteins, nucleic acids, and peptides in both folded and unfolded conformations. A cubic-spline function is introduced to guarantee good numerical behavior of the new density function. Our test results show that the average relative energy errors computed with the revised density function are uniformly lower than 1% for both training and test molecules with different sizes and conformations. Our transferability analysis shows that the performance of the new method is mostly size and conformation independent. A detailed analysis further shows that the numerical forces computed with the revised density function converge better with respect to the grid spacing and are numerically more stable in tested peptides.
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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.