• APBS

  • Referenced in 87 articles [sw05766]
  • important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ... rational drug design, and biomolecular titration studies...
  • AMBER

  • Referenced in 54 articles [sw01333]
  • programs for biomolecular simulation and analysis. They are designedto work well with each other...
  • NAMD

  • Referenced in 77 articles [sw03198]
  • code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects ... popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file...
  • GROMOS

  • Referenced in 30 articles [sw08091]
  • GROMOS Software Package for Biomolecular Simulations. GROMOS is an acronym of the GROningen MOlecular Simulation...
  • PBEQ-Solver

  • Referenced in 13 articles [sw17203]
  • uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference...
  • NAMD2

  • Referenced in 21 articles [sw09642]
  • molecular dynamics. Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding...
  • OpenMM

  • Referenced in 7 articles [sw19831]
  • OpenMM: A high performance toolkit for molecular simulation. Use it as a library ... Omnia suite of tools for predictive biomolecular simulation...
  • REACH

  • Referenced in 6 articles [sw00788]
  • package for residue-scale coarse-grained biomolecular simulation. The program calculates the force constants...
  • VMD

  • Referenced in 83 articles [sw18651]
  • program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built ... trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical...
  • ESES

  • Referenced in 3 articles [sw26786]
  • some of the most important tasks in biomolecular modeling and computation. Eulerian solvent excluded surface ... Cartesian grid, which is necessary for simulating many biomolecular electrostatic and ion channel models. However...
  • ProtoMS

  • Referenced in 1 article [sw27536]
  • ProtoMS: Monte Carlo Biomolecular Free Energy Simulation Program ... ProtoMS is a complete Monte Carlo biomolecular simulation program which is able to perform...
  • BIOMCSIM

  • Referenced in 2 articles [sw03003]
  • Monte Carlo simulation of biomolecular systems with BIOMCSIM...
  • PVM-AMBER

  • Referenced in 1 article [sw21840]
  • coordinate data exchange and processor synchronization. Test simulations performed for solvated peptide, protein, and lipid ... eight machines) for typical biomolecular simulation problems. PVM-AMBER is also easily and rapidly portable...
  • Spatkin

  • Referenced in 1 article [sw34203]
  • biomolecules. The tool is capable of simulating biomolecular interactions occurring...
  • MSMBuilder

  • Referenced in 2 articles [sw23802]
  • MSMBuilder: Statistical Models for Biomolecular Dynamics. MSMBuilder is a software package for building statistical models ... focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding...
  • STOCHSIM

  • Referenced in 6 articles [sw32181]
  • modelling of stochastic biomolecular processes. Summary: StochSim is a stochastic simulator for chemical reactions. Molecules...
  • ACEMD

  • Referenced in 7 articles [sw21783]
  • edge for molecular dynamics simulations. ACEMD is a production-class biomolecular dynamics (MD) engine supporting...
  • SloppyCell

  • Referenced in 3 articles [sw13614]
  • software environment for simulation and analysis of biomolecular networks. Features: support for much ... version 3; deterministic and stochastic dynamical simulations; sensitivity analysis without finite-difference derviatives; optimization methods...
  • pyPcazip

  • Referenced in 0 articles [sw20634]
  • analysis of molecular simulation data. The biomolecular simulation community is currently in need of novel...
  • BioGRID

  • Referenced in 8 articles [sw01699]
  • development of various interfaces to biomolecular applications and databases. The main task of Bio-GRID ... toolsets and user interfaces for both simulations and visualization of biomolecules were developed...