• APBS

  • Referenced in 92 articles [sw05766]
  • popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum ... electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional ... protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations...
  • TABI

  • Referenced in 29 articles [sw18194]
  • formulation for the electrostatic potential and its normal derivative on the molecular surface. The surface ... TABI solver is applied to compute the electrostatic solvation energy in two cases, the Kirkwood ... with non-uniform clusters adapted to the molecular surface. For the protein test case...
  • PDB2PQR

  • Referenced in 34 articles [sw13087]
  • continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from ... common tasks of preparing structures for continuum electrostatics calculations, including adding a limited number...
  • TMSmesh

  • Referenced in 20 articles [sw14719]
  • existing methods for surface generation used in molecular visualization and geometry analysis. Moreover, the meshes ... route to simulate electrostatic solvation of large-scale molecular systems. The binary version of TMSmesh...
  • PyGBe

  • Referenced in 5 articles [sw17642]
  • Python, GPUs and Boundary elements for biomolecular electrostatics. PyGBe—pronounced pigbē—is a Python code ... apply the boundary element method for molecular-electrostatics calculations in a continuum model. It computes...
  • MacMolPlt

  • Referenced in 3 articles [sw07039]
  • view orbitals, total electron densities and Molecular Electrostatic Potentials as 2D or 3D surfaces. Depending...
  • MIBPB

  • Referenced in 54 articles [sw08106]
  • software package, the MIBPB solver, for electrostatic analysis. The MIBPB has a unique feature that ... biomolecule and the solvent. For protein molecular surfaces, which may possess troublesome geometrical singularities...
  • PBEQ-Solver

  • Referenced in 14 articles [sw17203]
  • electrostatic potential contours using a novel online visualization tool based on MarvinSpace molecular visualization software...
  • DelPhiForce

  • Referenced in 2 articles [sw34189]
  • calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling...
  • TexMol

  • Referenced in 5 articles [sw13086]
  • sensitive level-of-detail hierarchy into our molecular representation, we communicate appropriate volume occupancy ... properties data (e.g. electrostatics potential) to be mapped onto the molecular surface, tying molecular structure...
  • TINKER

  • Referenced in 10 articles [sw04095]
  • OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang’s polarizable model ... flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments ... symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor ... novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better sampling...
  • Moldy

  • Referenced in 5 articles [sw01311]
  • ions in any mixture. Molecules or molecular ions are treated in the rigid-molecule approximation ... method is used to calculate long-ranged electrostatic forces...
  • ProtoMol

  • Referenced in 8 articles [sw10728]
  • molecular dynamics (MD) and of fast solvers for the force computation, particularly due to electrostatic...
  • Apbsmem

  • Referenced in 4 articles [sw22298]
  • membrane. Electrostatic forces are one of the primary determinants of molecular interactions. They help guide ... binding. A popular method for computing the electrostatic properties of biological systems is to numerically...
  • SCELib

  • Referenced in 5 articles [sw00831]
  • related molecular properties of a polyatomic molecular system within the Single Centre of Expansion ... reference. The resulting SCE wavefunction, electron density, electrostatic and exchange/correlation potentials can then be used ... Program Interface (AFI) to describe the target molecular system in electron-molecule scattering calculations...
  • DensToolKit

  • Referenced in 0 articles [sw20061]
  • localized electrons detector (LED), information entropy, molecular electrostatic potential, kinetic energy densities...
  • MOLDEN

  • Referenced in 4 articles [sw20678]
  • molecular vibrations. It can calculate and display the true or Multipole Derived Electrostatic Potential...
  • UHBD

  • Referenced in 8 articles [sw08088]
  • Electrostatics and diffusion of molecules in solution – simulations with the University-of-Houston Brownian dynamics ... with a flexible substrate and target, and molecular mechanics/dynamics calculations using a continuum solvent. These...
  • DelEnsembleElec

  • Referenced in 1 article [sw21782]
  • current biological interest, obtaining the ensemble-averaged electrostatic properties of the two major influenza virus ... atom molecular dynamics trajectories. The differences between the ensemble-averaged electrostatics and those obtained from...
  • PAFMPB

  • Referenced in 6 articles [sw16770]
  • tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement ... total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented...