PDB2PQR

swMATH13087MaRDI QIDQ25005FDOQ25005

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Cited In (36)

• A fast direct solver for structured linear systems by recursive skeletonization
• Biomolecular surface construction by PDE transform
• Quantum dynamics in continuum for proton transport. II: Variational solvent-solute interface
• Automated parallel and body-fitted mesh generation in finite element simulation of macromolecular systems
• A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
• Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules
• On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
• Numerical methods for the Poisson-Fermi equation in electrolytes
• An implicit boundary integral method for computing electric potential of macromolecules in solvent
• Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules
• Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling
• Efficient calculation of fully resolved electrostatics around large biomolecules
• Stabilized finite element methods to simulate the conductances of ion channels
• High-order fractional partial differential equation transform for molecular surface construction
• Second-order Poisson-Nernst-Planck solver for ion transport
• A domain decomposition method for the polarizable continuum model based on the solvent excluded surface
• Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
• Nanoscale thermodynamics of biological interfacial tension
• Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the \textsc{PyGBe} code
• SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
• A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers
• Adaptive finite element modeling techniques for the Poisson-Boltzmann equation
• Accurate gradient approximation for complex interface problems in 3D by an improved coupling interface method
• Using computational approaches to study dengue virus capsid assembly
• A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
• A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule
• Accurate p\(K_a\) computation using matched interface and boundary (MIB) method based Poisson-Boltzmann solver
• Variational multiscale models for charge transport
• Poisson-Fermi formulation of nonlocal electrostatics in electrolyte solutions
• An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics
• A stochastic solver of the generalized Born model
• INN: interfaced neural networks as an accessible meshless approach for solving interface PDE problems
• Efficient and qualified mesh generation for Gaussian molecular surface using adaptive partition and piecewise polynomial approximation
• DelEnsembleElec: computing ensemble-averaged electrostatics using DelPhi

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