• TINKER

  • Referenced in 11 articles [sw04095]
  • including several generalized Born (GB/SA) models, generalized Kirkwood implicit solvation for AMOEBA, an interface...
  • APBS

  • Referenced in 95 articles [sw05766]
  • most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media ... protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations...
  • QTM

  • Referenced in 3 articles [sw14198]
  • Triangle/Tetrahedral Meshes) constructs quality meshes for implicit solvation models of biomolecular structures starting from atomic...
  • VASPsol

  • Referenced in 1 article [sw27046]
  • VASPsol: We implemented an implicit solvation model that describes the effect of electrostatics, cavitation...
  • SDPBS

  • Referenced in 7 articles [sw17208]
  • solvated biomolecules. The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model...
  • CAMPARI

  • Referenced in 0 articles [sw39269]
  • ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing...
  • NSOL

  • Referenced in 2 articles [sw21620]
  • included as implicit solvation effects, such as continuum model using distance dependent dielectric constant. While...
  • LS-VISM

  • Referenced in 3 articles [sw16158]
  • implement numerical methods for a variational implicit-solvent model (VISM). The input of the package ... dielectric coefficients. The output includes estimated solvation free energies and optimal macroscopic solute–solvent interfaces...
  • TMSmesh

  • Referenced in 21 articles [sw14719]
  • numerical simulation of biomolecules, especially in implicit solvent modeling (e.g., see a review ... rise to a route to simulate electrostatic solvation of large-scale molecular systems. The binary...
  • PyGBe

  • Referenced in 5 articles [sw17642]
  • continuum model. It computes solvation energies for proteins modeled with any number of dielectric regions ... solving the Poisson-Boltzmann equation of the implicit-solvent model in integral form. PyGBe achieves...
  • Maple

  • Referenced in 5403 articles [sw00545]
  • The result of over 30 years of cutting...
  • Mathematica

  • Referenced in 6445 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 13702 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • ISIM

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

  • Referenced in 1336 articles [sw03258]
  • The NVIDIA® CUDA® Toolkit provides a comprehensive development...
  • PETSc

  • Referenced in 1594 articles [sw04012]
  • The Portable, Extensible Toolkit for Scientific Computation (PETSc...
  • TetGen

  • Referenced in 185 articles [sw04046]
  • TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator...
  • Gromacs

  • Referenced in 124 articles [sw04128]
  • GROMACS is a versatile package to perform molecular...
  • DOLFIN

  • Referenced in 203 articles [sw04313]
  • DOLFIN is a C++/Python library that functions...
  • FEniCS

  • Referenced in 856 articles [sw04314]
  • The FEniCS Project is a collaborative project for...