
TMSmesh
 Referenced in 20 articles
[sw14719]
 numerical simulation of biomolecules, especially in implicit solvent modeling (e.g., see a review...

APBS
 Referenced in 92 articles
[sw05766]
 most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media ... protein and proteinprotein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding...

PyGBe
 Referenced in 5 articles
[sw17642]
 model. It computes solvation energies for proteins modeled with any number of dielectric regions ... PoissonBoltzmann equation of the implicitsolvent model in integral form. PyGBe achieves both algorithmic...

SDPBS
 Referenced in 7 articles
[sw17208]
 equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein...

LSVISM
 Referenced in 3 articles
[sw16158]
 implement numerical methods for a variational implicitsolvent model (VISM). The input of the package...

SIMS
 Referenced in 2 articles
[sw21778]
 dielectric border between high dielectric solvent and the low dielectric molecular interior. The SIMS method ... used in a variety of implicit methods of modeling solvent effects. The SIMS program...

SELM
 Referenced in 3 articles
[sw17574]
 dynamic thermostats to extend implicitsolvent coarsegrained (ISCG) models by incorporating kinetic contributions...

NSOL
 Referenced in 2 articles
[sw21620]
 included as implicit solvation effects, such as continuum model using distance dependent dielectric constant. While ... methods that calculate solvation energy using solvent accessible surface area; ASP (atomic solvation parameters) model...

OPM
 Referenced in 2 articles
[sw33426]
 encourages open innovation and reproducible research for modeling and simulation of porous media processes ... fully implicit blackoil simulator that also supports solvent and polymer options. It is built...

ProFASi
 Referenced in 1 article
[sw30576]
 simulations and analyzing the generated data. The model implemented uses an allatom protein description ... degrees of freedom, and a simplified implicit solvent force field...

VASPsol
 Referenced in 1 article
[sw27046]
 VASPsol: We implemented an implicit solvation model that describes the effect of electrostatics, cavitation ... interaction between a solute and solvent into the planewave DFT code VASP. Our implementation...

ADOLC
 Referenced in 249 articles
[sw00019]
 ADOLC: Automatic Differentiation of C/C++. We present...

BoomerAMG
 Referenced in 195 articles
[sw00086]
 BoomerAMG: A parallel algebraic multigrid solver and preconditioner...

hypre
 Referenced in 306 articles
[sw00426]
 hypre is a software library for the solution...

LAPACK
 Referenced in 1695 articles
[sw00503]
 LAPACK is written in Fortran 90 and provides...

Matlab
 Referenced in 13460 articles
[sw00558]
 MATLAB® is a highlevel language and interactive...

UMFPACK
 Referenced in 412 articles
[sw00989]
 An ANSI C code for sparse LU factorization...

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...

ADIFOR
 Referenced in 254 articles
[sw02185]
 ADIFOR is a tool for the automatic differentiation...