APBS
From MaRDI portal
Cited in
(only showing first 100 items - show all)- Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
- Iterative convex quadratic approximation for global optimization in protein docking
- ``New-version-fast-multipole-method accelerated electrostatic calculations in biomolecular sys\-tems
- Fast analytical methods for macroscopic electrostatic models in biomolecular simulations
- A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
- Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann equation in numerical simulation of colloidal particle interactions
- Image charge methods for a three-dielectric-layer hybrid solvation model of biomolecules
- Modeling electrokinetic flows by the smoothed profile method
- A Poisson-Boltzmann solver on irregular domains with Neumann or Robin boundary conditions on non-graded adaptive grid
- Browndye: A software package for Brownian dynamics
- Radial basis collocation method and quasi-Newton iteration for nonlinear elliptic problems
- The de Rham-Hodge analysis and modeling of biomolecules
- A second-order discretization of the nonlinear Poisson-Boltzmann equation over irregular geometries using non-graded adaptive Cartesian grids
- Geometry-guided computation of 3D electrostatics for large biomolecules
- Regularization of Poisson-Boltzmann-type equations with singular source terms using the range-separated tensor format
- A weighted adaptive least-squares finite element method for the Poisson-Boltzmann equation
- Model reduction-based initialization methods for solving the Poisson-Nernst-Planck equations in three-dimensional ion channel simulations
- A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
- Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules
- scientific article; zbMATH DE number 5669486 (Why is no real title available?)
- Progress in developing Poisson-Boltzmann equation solvers
- The calculus of boundary variations and the dielectric boundary force in the Poisson-Boltzmann theory for molecular solvation
- Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules
- On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
- FEM and BEM parallel processing: theory and applications – a bibliography (1996‐2002)
- An implicit boundary integral method for computing electric potential of macromolecules in solvent
- The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
- Stability of a Cylindrical Solute-Solvent Interface: Effect of Geometry, Electrostatics, and Hydrodynamics
- New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
- Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity
- Poisson-Boltzmann equation boundary conditions for biological applications
- On the convergence of an optimal additive Schwarz method for parallel adaptive finite elements
- A boundary element formulation of protein electrostatics with explicit ions
- ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules
- Efficient calculation of fully resolved electrostatics around large biomolecules
- A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
- Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation
- A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
- A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
- scientific article; zbMATH DE number 5262917 (Why is no real title available?)
- Some random batch particle methods for the Poisson-Nernst-Planck and Poisson-Boltzmann equations
- Local averaging based a posteriori finite element error control for quasilinear elliptic problems with application to electrical potential computation
- A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
- ISIM
- AMBER
- NAMD
- PRONTO3D
- Gromacs
- CHARMM
- PetFMM
- Delphi
- Browndye
- FISHPAK
- Macrodox
- MIBPB
- SDA
- PIM
- UHBD
- AFMPB
- FFTSVD
- Fastcap
- LINCS
- PyMOL
- FEtk
- GAMER
- PHG
- F2Dock
- SETTLE
- MolEnergy
- PDB2PQR
- TexMol
- MCCE2
- QTM
- TMSmesh
- BIEPACK
- PAFMPB
- DelPhi Web Server
- PBEQ-Solver
- SDPBS
- PyGBe
- TOMOBFLOW
- TABI
- VMD
- SG
- FreeSASA
- Apbsmem
- SMPBS
- ESES
- ReebHanTun
- Intersurf
- Lis
- DelPhiPKa
- MPBEC
- DAFMPB
- A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations
- nuSMPBIC
- Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
- A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent
- Two-scale finite element Green's function approximations with applications to electrostatic potential computation
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