• PDB2PQR

  • Referenced in 33 articles [sw13087]
  • tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. However ... Bank and the assignment of parameters to biomolecular structures. To address this problem, we have developed ... continuum electrostatics calculations, including adding a limited number of missing heavy atoms to biomolecular structures ... biological community of continuum electrostatics analyses of biomolecular systems...
  • APBS

  • Referenced in 91 articles [sw05766]
  • media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation...
  • AFMPB

  • Referenced in 10 articles [sw08875]
  • multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems. It is described an adaptive ... multipole Poisson-Boltzmann solver for computing the electrostatics in biomolecules. This solver combines the fast...
  • PyGBe

  • Referenced in 4 articles [sw17642]
  • Python, GPUs and Boundary elements for biomolecular electrostatics. PyGBe—pronounced pigbē—is a Python code...
  • ESES

  • Referenced in 4 articles [sw26786]
  • which is necessary for simulating many biomolecular electrostatic and ion channel models. However, large biomolecules...
  • PBEQ-Solver

  • Referenced in 13 articles [sw17203]
  • PBEQ-Solver for online visualization of electrostatic potential of biomolecules. PBEQ-Solver provides ... read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential ... energy, (ii) protein–protein (DNA or RNA) electrostatic interaction energy ... Solver uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite...
  • MPBEC

  • Referenced in 1 article [sw38537]
  • MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations. One of the most used and efficient ... approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann ... easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC ... approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools...
  • DAFMPB

  • Referenced in 1 article [sw40371]
  • electrostatic potentials and forces, and total solvation-free energy in biomolecular systems modeled...
  • LS-VISM

  • Referenced in 3 articles [sw16158]
  • software package for the analysis of biomolecular solvation. The package collects computer codes that implement ... review the VISM with various descriptions of electrostatics. We also review our numerical methods that...
  • BEMLIB

  • Referenced in 106 articles [sw00005]
  • BEMLIB is a boundary-element software library of...
  • Matlab

  • Referenced in 12983 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • TNPACK

  • Referenced in 42 articles [sw00970]
  • We present a FORTRAN package of subprograms for...
  • ISIM

  • Referenced in 4 articles [sw01100]
  • SimTK ISIM interface a simple Java graphical user...
  • AMBER

  • Referenced in 57 articles [sw01333]
  • AmberTools is a set of programs for biomolecular...
  • FreeFem++

  • Referenced in 1234 articles [sw01436]
  • FreeFem++ is an implementation of a language dedicated...
  • NAMD

  • Referenced in 79 articles [sw03198]
  • NAMD is a parallel molecular dynamics code designed...
  • CUDA

  • Referenced in 1275 articles [sw03258]
  • The NVIDIA® CUDA® Toolkit provides a comprehensive development...
  • PETSc

  • Referenced in 1252 articles [sw04012]
  • The Portable, Extensible Toolkit for Scientific Computation (PETSc...
  • TetGen

  • Referenced in 165 articles [sw04046]
  • TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator...
  • FFTW

  • Referenced in 516 articles [sw04126]
  • FFTW is a C subroutine library for computing...