
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 ... proteinprotein 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 PoissonBoltzmann 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...

LSVISM
 Referenced in 3 articles
[sw16158]
 implement numerical methods for a variational implicitsolvent 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 largescale 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 PoissonBoltzmann equation of the implicitsolvent 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 highlevel 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 DelaunayBased 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...