• APBS

  • Referenced in 87 articles [sw05766]
  • most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media ... Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation...
  • MIBPB

  • Referenced in 49 articles [sw08106]
  • MIBPB: A software package for electrostatic analysis. The Poisson–Boltzmann equation (PBE) is an established ... model for the electrostatic analysis of biomolecules. The development of advanced computational techniques ... software package, the MIBPB solver, for electrostatic analysis. The MIBPB has a unique feature that...
  • PDB2PQR

  • Referenced in 33 articles [sw13087]
  • pipeline for the setup of Poisson–Boltzmann electrostatics calculations. Continuum solvation models, such as Poisson ... popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. However ... radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing ... common tasks of preparing structures for continuum electrostatics calculations, including adding a limited number...
  • TABI

  • Referenced in 21 articles [sw18194]
  • accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules. We present a treecode ... accelerated boundary integral (TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson ... well-conditioned boundary integral formulation for the electrostatic potential and its normal derivative ... TABI solver is applied to compute the electrostatic solvation energy in two cases, the Kirkwood...
  • PBEQ-Solver

  • Referenced in 13 articles [sw17203]
  • PBEQ-Solver for online visualization of electrostatic potential of biomolecules. PBEQ-Solver provides ... Boltzmann (PB) equations and interactively visualize the electrostatic potential. PBEQ-Solver calculates (i) electrostatic potential ... energy, (ii) protein–protein (DNA or RNA) electrostatic interaction energy ... users. Users can interactively inspect the calculated electrostatic potential on the solvent-accessible surface...
  • SPRINT2D

  • Referenced in 25 articles [sw00904]
  • procedure for a Burgers’ equations problem, an electrostatics problem from elastohydrodynamic lubrication, and a challenging...
  • VORPAL

  • Referenced in 19 articles [sw02597]
  • running computationally intensive plasma, electromagnetic and electrostatic problems. VSim enables you to switch easily between...
  • TMSmesh

  • Referenced in 16 articles [sw14719]
  • gives rise to a route to simulate electrostatic solvation of large-scale molecular systems...
  • TINKER

  • Referenced in 10 articles [sw04095]
  • flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments ... novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better sampling...
  • SUGAR

  • Referenced in 12 articles [sw15321]
  • world of integrated circuit simulation. Beams, electrostatic gaps, circuit elements, and other elements are modeled...
  • DelPhi Web Server

  • Referenced in 7 articles [sw17209]
  • server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes. Here ... server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential...
  • neBEM

  • Referenced in 7 articles [sw06382]
  • neBEM solver has been used to solve electrostatic problems having three-dimensional edges and corners ... accuracy. We then consider several problems of electrostatics containing edges and singularities of various orders...
  • AFMPB

  • Referenced in 7 articles [sw08875]
  • fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems. It is described ... multipole Poisson-Boltzmann solver for computing the electrostatics in biomolecules. This solver combines the fast...
  • FFTSVD

  • Referenced in 10 articles [sw08886]
  • algorithm that is well suited for solving electrostatics problems that arise in traditional...
  • ORB5

  • Referenced in 10 articles [sw10369]
  • ORB5, is presented. It solves the gyrokinetic electrostatic equations including zonal flows in axisymmetric magnetic...
  • MaxFEM

  • Referenced in 10 articles [sw12800]
  • applications that can address problems in electrostatics, current, and eddy-currents, magnetostatics in two and/or...
  • POT4A

  • Referenced in 9 articles [sw01206]
  • program was developed to solve problems in electrostatics but can also be applied in other...
  • BETL

  • Referenced in 9 articles [sw12389]
  • engineering applications. Prominent examples are, e.g., electrostatic or thermal models as well as the scattering...
  • SDPBS

  • Referenced in 6 articles [sw17208]
  • SDPBS web server for calculation of electrostatics of ionic solvated biomolecules. The Poisson-Boltzmann equation ... important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. We recently...