• PDB2PQR

  • Referenced in 35 articles [sw13087]
  • popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. However ... complete structural data as well as force field parameters such as atomic charges and radii ... Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic ... common tasks of preparing structures for continuum electrostatics calculations, including adding a limited number...
  • Moldy

  • Referenced in 5 articles [sw01311]
  • used to calculate long-ranged electrostatic forces...
  • DelPhiForce

  • Referenced in 2 articles [sw34189]
  • DelPhiForce web server: electrostatic forces and energy calculations and visualization. Summary: Electrostatic force ... macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many ... server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables ... modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output...
  • Apbsmem

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

  • Referenced in 8 articles [sw10728]
  • fast solvers for the force computation, particularly due to electrostatic interactions. Several new and efficient...
  • MMM2D

  • Referenced in 4 articles [sw18357]
  • method to accurately calculate the electrostatic energy and forces on charges being distributed...
  • DropBot

  • Referenced in 1 article [sw27303]
  • control system with precise control of electrostatic driving force and instantaneous drop velocity measurement ... forces), and (2) application of constant electrostatic driving forces through compensation for amplifier-loading...
  • LPMD

  • Referenced in 1 article [sw12495]
  • unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written ... Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function...
  • MMM1D

  • Referenced in 2 articles [sw18358]
  • method to accurately calculate the electrostatic energy and forces on charges in a system with...
  • DAMQT

  • Referenced in 1 article [sw22183]
  • density, density deformations, electrostatic potential and field, and Hellmann–Feynman forces. Algorithms for the partition ... like density deformations, electrostatic potential and field and Hellmann–Feynman forces have been improved...
  • DAFMPB

  • Referenced in 1 article [sw40371]
  • rapid evaluation of the electrostatic potentials and forces, and total solvation-free energy in biomolecular...
  • TINKER

  • Referenced in 11 articles [sw04095]
  • field. Parameter sets for other widely-used force fields are under consideration for future releases ... flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments...
  • SPARC

  • Referenced in 6 articles [sw22290]
  • Specifically, utilizing a local reformulation of the electrostatics, the Chebyshev polynomial filtered self-consistent field ... local component of the force, we develop a framework using the finite-difference representation that...
  • DelPhi Web Server

  • Referenced in 8 articles [sw17209]
  • calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric ... calculations can be done with user selected force field parameters being either Charmm22, Amber98...
  • PIC-MCC

  • Referenced in 7 articles [sw03085]
  • model with realistic spatial dependencies of the electrostatic field. It is shown that ... close to the field where the electric force on an electron equals the maximum frictional...
  • MOLDEN

  • Referenced in 4 articles [sw20678]
  • atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface. Molden ... combined Amber (protein) and GAFF (small molecules) force fields. Atom typing can be done automatically...
  • PEPC

  • Referenced in 1 article [sw33269]
  • forces is presented. It can be used as a library for applications involving electrostatics...
  • transiesta

  • Referenced in 8 articles [sw33754]
  • calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale ... self-consistency and the solution of the electrostatic problem is taken into account using nonequilibrium...
  • Macrodox

  • Referenced in 2 articles [sw08087]
  • Data Bank. Such properties would include surrounding electrostatic fields, dipole moment, radius of gyration, titration ... methodology, the program would allow an automated force-guided search of docked conformers which would ... which are less able to accurately handle electrostatic interactions. Additionally the program is able...
  • SDA

  • Referenced in 4 articles [sw08089]
  • absence of long-range forces (Northrup, S. H., and H. P. Erickson. 1992. Kinetics ... Fersht. 1996. Rapid, electrostatically assisted association of proteins. Nat. Struct. Biol. 3:427–431), implying...