ArticleJournal of computational chemistry2011
MIBPB: a software package for electrostatic analysis.
Article in Journal of computational chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
65 citing papers in PubMed.
- Persistent sheaf Laplacian analysis of protein stability and solubility changes upon mutation.Protein science : a publication of the Protein Society · 2026Article
- AmberTorchPB: A Unified Framework for Poisson-Boltzmann-Based Reaction Field Energy Calculation via Tensor Computation.Journal of chemical theory and computation · 2026Article
- A DNN Biophysics Model with Topological and Electrostatic Features.Journal of chemical information and modeling · 2026Article
- On generalizing the induced surface charge method to heterogeneous Poisson-Boltzmann models for electrostatic free energy calculation.Journal of computational physics · 2026Article
- Topological machine learning for protein-nucleic acid binding affinity changes upon mutation.Machine learning: science and technology · 2025Article
- End-to-End Modeling of Reaction Field Energy Using Data-Driven Geometric Graph Neural Networks.Journal of chemical theory and computation · 2025Article
- Poisson-Boltzmann-based machine learning model for electrostatic analysis.Biophysical journal · 2024Article
- Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains.The journal of physical chemistry. B · 2024Article
- Bridging Eulerian and Lagrangian Poisson-Boltzmann solvers by ESES.Journal of computational chemistry · 2024Article
- Integration of persistent Laplacian and pre-trained transformer for protein solubility changes upon mutation.Computers in biology and medicine · 2024Article
- Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential.Journal of computational physics · 2024Article
- Article
- A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules.ACS omega · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- A Physics-Guided Neural Network for Predicting Protein-Ligand Binding Free Energy: From Host-Guest Systems to the PDBbind Database.Biomolecules · 2022Article
- Geometric algebra generation of molecular surfaces.Journal of the Royal Society, Interface · 2022Article
- MLIMC: Machine Learning-Based Implicit-Solvent Monte Carlo.Chinese journal of chemical physics · 2021Article
- Multivalent Ion-Mediated Attraction between Like-Charged Colloidal Particles: Nonmonotonic Dependence on the Particle Charge.ACS omega · 2021Article
- The de Rham-Hodge Analysis and Modeling of Biomolecules.Bulletin of mathematical biology · 2020Article
- Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.Journal of chemical theory and computation · 2020Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The Poisson-Boltzmann equation (PBE) is an established model for the electrostatic analysis of biomolecules. The development of advanced computational techniques for the solution of the PBE has been an important topic in the past two decades. This article presents a matched interface and boundary (MIB)-based PBE software package, the MIBPB solver, for electrostatic analysis. The MIBPB has a unique feature that it is the first interface technique-based PBE solver that rigorously enforces the solution and flux continuity conditions at the dielectric interface between the biomolecule and the solvent. For protein molecular surfaces, which may possess troublesome geometrical singularities, the MIB scheme makes the MIBPB by far the only existing PBE solver that is able to deliver the second-order convergence, that is, the accuracy increases four times when the mesh size is halved. The MIBPB method is also equipped with a Dirichlet-to-Neumann mapping technique that builds a Green's function approach to analytically resolve the singular charge distribution in biomolecules in order to obtain reliable solutions at meshes as coarse as 1 Å--whereas it usually takes other traditional PB solvers 0.25 Å to reach similar level of reliability. This work further accelerates the rate of convergence of linear equation systems resulting from the MIBPB by using the Krylov subspace (KS) techniques. Condition numbers of the MIBPB matrices are significantly reduced by using appropriate KS solver and preconditioner combinations. Both linear and nonlinear PBE solvers in the MIBPB package are tested by protein-solvent solvation energy calculations and analysis of salt effects on protein-protein binding energies, respectively.
Indexed as
Identifiers
What OpenQuestion holds
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.