tabipb

MaRDI QIDQ5975031swMATHFDO

Official website https://sourceforge.net/projects/tabipb/

Described by source

• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• Computing electrostatic binding energy with the TABI Poisson-Boltzmann solver

Cited in

(72)

• Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
• HSMA3D
• A kernel-independent treecode for general Rotne-Prager-Yamakawa tensor
• The de Rham-Hodge analysis and modeling of biomolecules
• A kernel-independent treecode based on barycentric Lagrange interpolation
• A treecode based on barycentric Hermite interpolation for electrostatic particle interactions
• An asymptotic preserving Maxwell solver resulting in the Darwin limit of electrodynamics
• On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
• An implicit boundary integral method for computing electric potential of macromolecules in solvent
• An \(O(N \log N)\) hierarchical random compression method for kernel matrices by sampling partial matrix entries
• On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• A computational model of protein induced membrane morphology with geodesic curvature driven protein-membrane interface
• Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation
• A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
• NAMD
• APBS
• CHARMM
• MIBPB
• UHBD
• AFMPB
• FFTSVD
• HOT
• AFEPack
• PDB2PQR
• LBIE
• TMSmesh
• pvfmm
• BIEPACK
• PAFMPB
• DelPhi Web Server
• PBEQ-Solver
• ASKIT
• SDPBS
• FMMLIB3D
• PyGBe
• MLAPM
• TABI
• VMD
• Apbsmem
• Algorithm 967
• SMPBS
• ESES
• ScalFMM
• STFMMLIB3D
• ReebHanTun
• Afivo
• DAFMPB
• RPYFMM
• QTFier
• An integral equation formulation of the \(N\)-body dielectric spheres problem. II: Complexity analysis
• A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations
• nuSMPBIC
• Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
• Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation
• VCMM
• Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the \textsc{PyGBe} code
• A Treecode Algorithm for 3D Stokeslets and Stresslets
• Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
• SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
• DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
• tricubic-treecodes
• A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation
• Efficient implementation of the Barnes-Hut octree algorithm for Monte Carlo simulations of charged systems
• NanoShaper
• A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models
• Harmonic Surface Mapping Algorithm for Electrostatic Potentials in an Atomistic/Continuum Hybrid Model for Electrolyte Solutions
• Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
• Accurate p\(K_a\) computation using matched interface and boundary (MIB) method based Poisson-Boltzmann solver
• Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
• Multi-core CPU or GPU-accelerated multiscale modeling for biomolecular complexes
• DelPhi

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