• VMD

  • Referenced in 90 articles [sw18651]
  • displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting...
  • NAMD

  • Referenced in 80 articles [sw03198]
  • high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales...
  • PDB2PQR

  • Referenced in 35 articles [sw13087]
  • community of continuum electrostatics analyses of biomolecular systems...
  • NAMD2

  • Referenced in 21 articles [sw09642]
  • dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However...
  • AFMPB

  • Referenced in 12 articles [sw08875]
  • Boltzmann solver for calculating electrostatics in biomolecular systems. It is described an adaptive fast multipole...
  • Cytoscape

  • Referenced in 82 articles [sw09080]
  • open source software project for integrating biomolecular interaction networks with high-throughput expression data ... unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape...
  • ProDy

  • Referenced in 4 articles [sw24072]
  • structures experimentally resolved for a given biomolecular system, and for comparison of these variations with...
  • MOLE

  • Referenced in 3 articles [sw18622]
  • Tests on a wide variety of biomolecular systems including gramicidine, acetylcholinesterase, cytochromes P450, potassium channels...
  • BIOMCSIM

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

  • Referenced in 1 article [sw40371]
  • total solvation-free energy in biomolecular systems modeled by the linearized Poisson-Boltzmann (LPB) equation...
  • THOR

  • Referenced in 1 article [sw07915]
  • study of solids and biomolecular systems. It is based on a hybrid approach which makes...
  • BisoGenet

  • Referenced in 2 articles [sw35192]
  • visualization and analysis of biomolecular relationships. The system consists of three tiers. In the data...
  • BioSG

  • Referenced in 1 article [sw18648]
  • Embedding Biomolecular Information in a Scene Graph System. We present the Bio Scene Graph (BioSG ... visualization of biomolecular structures based on the scene graph system OpenSG. The hierarchical model...
  • SloppyCell

  • Referenced in 3 articles [sw13614]
  • analysis of biomolecular networks. Features: support for much of the Systems Biology Markup Language (SBML...
  • ACEMD

  • Referenced in 7 articles [sw21783]
  • dynamics simulations. ACEMD is a production-class biomolecular dynamics (MD) engine supporting CHARMM and AMBER ... ns/day for all-atom protein systems with over 23 000 atoms. We provide a validation...
  • CytoCtrlAnalyser

  • Referenced in 1 article [sw34201]
  • controllability of biomolecular networks can result in profound knowledge about molecular biological systems. However, there ... platform for analyzing controllability of biomolecular networks although various algorithms for analyzing complex network controllability...
  • REACH

  • Referenced in 6 articles [sw00788]
  • program package for residue-scale coarse-grained biomolecular simulation. The program calculates the force constants ... procedure without requiring iterative fits and avoiding system dependence...
  • MPBEC

  • Referenced in 1 article [sw38537]
  • MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations. One of the most used and efficient ... approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann ... depending on the complexity of the biological system, to successfully obtain the numerical solution ... easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC...
  • RPYFMM

  • Referenced in 4 articles [sw40025]
  • Rotne–Prager–Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm ... show that the interactions for a molecular system of 15 million particles (beads...
  • LC-GAP

  • Referenced in 1 article [sw22566]
  • approach, we present LC-GAP, a new system for generating atomic potentials through machine learning ... Tests on the QM7, QM7b and GDB9 biomolecular datasets demonstrate that potentials created with...