PDB2PQR
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Cited in
(72)- 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
- Numerical methods for the Poisson-Fermi equation in electrolytes
- Fast and scalable algorithms for constructing solvent-excluded surfaces of large biomolecules
- On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
- An implicit boundary integral method for computing electric potential of macromolecules in solvent
- 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
- A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules
- Stabilized finite element methods to simulate the conductances of ion channels
- Efficient calculation of fully resolved electrostatics around large biomolecules
- Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling
- High-order fractional partial differential equation transform for molecular surface construction
- APBS
- CHARMM
- Delphi
- MIBPB
- UHBD
- FEtk
- GAMER
- PHG
- F2Dock
- MolEnergy
- TexMol
- TMSmesh
- AQUASOL
- DelPhi Web Server
- PBEQ-Solver
- SDPBS
- PyGBe
- TABI
- VMD
- SG
- FreeSASA
- DelEnsembleElec
- Medit
- MetaMol
- phgSurfaceCut
- SIMS
- Apbsmem
- SMPBS
- ESES
- DelPhiForce
- Second-order Poisson-Nernst-Planck solver for ion transport
- CHARMM36m
- DAFMPB
- nuSMPBIC
- A domain decomposition method for the polarizable continuum model based on the solvent excluded surface
- tabipb
- VCMM
- Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
- Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the \textsc{PyGBe} code
- Nanoscale thermodynamics of biological interfacial tension
- 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
- DelPhi
- 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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