• PDB2PQR

  • Referenced in 32 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 85 articles [sw05766]
  • media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation...
  • AFMPB

  • Referenced in 7 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...
  • 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...
  • PyGBe

  • Referenced in 3 articles [sw17642]
  • Python, GPUs and Boundary elements for biomolecular electrostatics. PyGBe—pronounced pigbē—is a Python code...
  • ESES

  • Referenced in 3 articles [sw26786]
  • which is necessary for simulating many biomolecular electrostatic and ion channel models. However, large biomolecules...
  • 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 96 articles [sw00005]
  • BEMLIB is a boundary-element software library of...
  • Matlab

  • Referenced in 11496 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • TNPACK

  • Referenced in 39 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 53 articles [sw01333]
  • AmberTools is a set of programs for biomolecular...
  • NAMD

  • Referenced in 77 articles [sw03198]
  • NAMD is a parallel molecular dynamics code designed...
  • CUDA

  • Referenced in 1136 articles [sw03258]
  • The NVIDIA® CUDA® Toolkit provides a comprehensive development...
  • PETSc

  • Referenced in 1092 articles [sw04012]
  • The Portable, Extensible Toolkit for Scientific Computation (PETSc...
  • FFTW

  • Referenced in 450 articles [sw04126]
  • FFTW is a C subroutine library for computing...
  • Gromacs

  • Referenced in 113 articles [sw04128]
  • GROMACS is a versatile package to perform molecular...
  • DOLFIN

  • Referenced in 152 articles [sw04313]
  • DOLFIN is a C++/Python library that functions...
  • FEniCS

  • Referenced in 476 articles [sw04314]
  • The FEniCS Project is a collaborative project for...
  • SWIG

  • Referenced in 43 articles [sw04607]
  • An extensible compiler for creating scriptable scientific software...