• APBS

  • Referenced in 92 articles [sw05766]
  • kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand...
  • MIBPB

  • Referenced in 54 articles [sw08106]
  • MIBPB package are tested by protein–solvent solvation energy calculations and analysis of salt effects...
  • TABI

  • Referenced in 29 articles [sw18194]
  • integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules. We present a treecode-accelerated boundary ... integral (TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson-Boltzmann equation ... solver is applied to compute the electrostatic solvation energy in two cases, the Kirkwood sphere ... solvated protein. We present the error, CPU time, and memory usage, and compare results...
  • PDB2PQR

  • Referenced in 34 articles [sw13087]
  • setup of Poisson–Boltzmann electrostatics calculations. Continuum solvation models, such as Poisson–Boltzmann and Generalized...
  • TMSmesh

  • Referenced in 20 articles [sw14719]
  • rise to a route to simulate electrostatic solvation of large-scale molecular systems. The binary...
  • Packmol

  • Referenced in 15 articles [sw13408]
  • molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures...
  • TINKER

  • Referenced in 10 articles [sw04095]
  • electrostatics with explicit dipole polarizability, various continuum solvation treatments including several generalized Born (GB/SA) models ... generalized Kirkwood implicit solvation for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, efficient...
  • ARVO

  • Referenced in 14 articles [sw00049]
  • spheres via analytic equations. For calculating the solvation energy of proteins, hydration effects, drug binding...
  • PBEQ-Solver

  • Referenced in 14 articles [sw17203]
  • PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein–protein...
  • PAFMPB

  • Referenced in 6 articles [sw16770]
  • automatic surface meshing for calculation of molecular solvation free energy. We present PAFMPB, an updated ... software package for fast calculation of molecular solvation-free energy. The new version ... package provides fast calculation of the total solvation-free energy, including the PB electrostatic...
  • SDPBS

  • Referenced in 7 articles [sw17208]
  • server for calculation of electrostatics of ionic solvated biomolecules. The Poisson-Boltzmann equation...
  • LS-VISM

  • Referenced in 3 articles [sw16158]
  • software package for analysis of biomolecular solvation. We introduce a software package for the analysis ... biomolecular solvation. The package collects computer codes that implement numerical methods for a variational implicit ... dielectric coefficients. The output includes estimated solvation free energies and optimal macroscopic solute–solvent interfaces ... that are obtained by minimizing the VISM solvation free-energy functional among all possible solute...
  • BALL

  • Referenced in 5 articles [sw10727]
  • well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures...
  • PyGBe

  • Referenced in 5 articles [sw17642]
  • calculations in a continuum model. It computes solvation energies for proteins modeled with any number...
  • NSOL

  • Referenced in 2 articles [sw21620]
  • program of molecular surface area, volume, and solvation energy. In computer simulation of proteins ... such as MD and/or MC, conformational energy + solvation energy calculation is needed. However, solvation energy ... included as implicit solvation effects, such as continuum model using distance dependent dielectric constant. While ... there exist two methods that calculate solvation energy using solvent accessible surface area; ASP (atomic...
  • BOSS

  • Referenced in 2 articles [sw27537]
  • pure liquid, free energies of solvation, effects of solvation on relative energies of conformers, changes ... free energies of solvation along reaction paths, and structures and relative free energies of binding...
  • QTM

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

  • Referenced in 3 articles [sw17113]
  • most popular approaches to modeling the solvation of molecules. It assumes a continuum model...
  • VASPsol

  • Referenced in 1 article [sw27046]
  • VASPsol: We implemented an implicit solvation model that describes the effect of electrostatics, cavitation ... efficient means to calculate the effects of solvation on molecules and crystal surfaces as well ... reaction barriers. The strength of our solvation model implementation is its capability to handle large...
  • MDVRY

  • Referenced in 2 articles [sw00566]
  • computer time and allows to study polarized solvated proteins at a very low CPU cost...