PDB2PQR
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Related Items (36)
Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling ⋮ Biomolecular surface construction by PDE transform ⋮ Efficient calculation of fully resolved electrostatics around large biomolecules ⋮ Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface ⋮ A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule ⋮ Stabilized finite element methods to simulate the conductances of ion channels ⋮ SDPBS web server for calculation of electrostatics of ionic solvated biomolecules ⋮ Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the \textsc{PyGBe} code ⋮ Numerical methods for the Poisson-Fermi equation in electrolytes ⋮ New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics ⋮ Accurate gradient approximation for complex interface problems in 3D by an improved coupling interface method ⋮ A domain decomposition method for the polarizable continuum model based on the solvent excluded surface ⋮ Poisson-Fermi formulation of nonlocal electrostatics in electrolyte solutions ⋮ Using computational approaches to study dengue virus capsid assembly ⋮ Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation ⋮ Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation ⋮ DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi ⋮ A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver ⋮ An implicit boundary integral method for computing electric potential of macromolecules in solvent ⋮ Automated Parallel and Body-Fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems ⋮ Variational Multiscale Models for Charge Transport ⋮ Efficient and Qualified Mesh Generation for Gaussian Molecular Surface Using Adaptive Partition and Piecewise Polynomial Approximation ⋮ A Fast Direct Solver for Structured Linear Systems by Recursive Skeletonization ⋮ Accurate PKa Computation Using Matched Interface and Boundary (MIB) Method Based Poisson-Boltzmann Solver ⋮ A biomolecular electrostatics solver using python, GPUs and boundary elements that can handle solvent-filled cavities and stern layers ⋮ Second-order Poisson-Nernst-Planck solver for ion transport ⋮ Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity ⋮ A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules ⋮ A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference ⋮ Nanoscale thermodynamics of biological interfacial tension ⋮ An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson–Boltzmann-Based Molecular Electrostatics ⋮ On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver ⋮ Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules ⋮ INN: interfaced neural networks as an accessible meshless approach for solving interface PDE problems ⋮ High-order fractional partial differential equation transform for molecular surface construction ⋮ A Stochastic Solver of the Generalized Born Model
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