ArticleJournal of chemical information and modeling2015
Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation.
Article in Journal of chemical information and modeling, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed.
- Article
- Article
- Inhibitory Potential of the Truncated Isoforms on Glutamate Transporter Oligomerization Identified by Computational Analysis of Gene-Centric Isoform Maps.Pharmaceutical research · 2024Article
- Identification of GαScientific reports · 2024Article
- 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
- SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic.Journal of cellular biochemistry · 2022Article
- Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations.Journal of chemical theory and computation · 2021Article
- Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor.The EMBO journal · 2020Article
- Improved Poisson-Boltzmann Methods for High-Performance Computing.Journal of chemical theory and computation · 2019Article
- Understanding G Protein Selectivity of Muscarinic Acetylcholine Receptors Using Computational Methods.International journal of molecular sciences · 2019Article
- NFBTA: A Potent Cytotoxic Agent against Glioblastoma.Molecules (Basel, Switzerland) · 2019Article
- Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies.Journal of chemical information and modeling · 2019Article
- Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units.Journal of chemical information and modeling · 2019Article
- Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aβ) Antibodies.The journal of physical chemistry. B · 2018Article
- A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins.International journal of molecular sciences · 2018Article
- The Model Structures of the Complement Component 5a Receptor (C5aR) Bound to the Native and EngineeredScientific reports · 2018Article
- 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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Continuum solvent models have been widely used in biomolecular modeling applications. Recently much attention has been given to inclusion of implicit membranes into existing continuum Poisson-Boltzmann solvent models to extend their applications to membrane systems. Inclusion of an implicit membrane complicates numerical solutions of the underlining Poisson-Boltzmann equation due to the dielectric inhomogeneity on the boundary surfaces of a computation grid. This can be alleviated by the use of the periodic boundary condition, a common practice in electrostatic computations in particle simulations. The conjugate gradient and successive over-relaxation methods are relatively straightforward to be adapted to periodic calculations, but their convergence rates are quite low, limiting their applications to free energy simulations that require a large number of conformations to be processed. To accelerate convergence, the Incomplete Cholesky preconditioning and the geometric multigrid methods have been extended to incorporate periodicity for biomolecular applications. Impressive convergence behaviors were found as in the previous applications of these numerical methods to tested biomolecules and MMPBSA calculations.
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.