• CGAL

  • Referenced in 374 articles [sw00118]
  • visualization, computer aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics...
  • Seq-Gen

  • Referenced in 31 articles [sw08310]
  • application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees ... acid sequences along a phylogeny, using common models ... substitution process. A range of models of molecular evolution are implemented including the general reversible ... commonly used (and computationally tractable) models of molecular sequence evolution. The paper cited above contains...
  • BEAST

  • Referenced in 49 articles [sw12588]
  • measured phylogenies using strict or relaxed molecular clock models. It can be used...
  • BioNetGen

  • Referenced in 57 articles [sw09072]
  • rule-based modeling of signal transduction based on the interactions of molecular domains. BioNetGen allows ... user to create a computational model that characterizes the dynamics of a signal transduction system ... molecular species that can arise during signaling and provides functions that relate model variables...
  • APBS

  • Referenced in 89 articles [sw05766]
  • most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media...
  • GRID Infoware

  • Referenced in 23 articles [sw04166]
  • data intensive computing applications (e.g, molecular modelling for drug design, brain activity analysis, and high...
  • LAMMPS

  • Referenced in 60 articles [sw05952]
  • Simulator) is a classical molecular dynamics code. LAMMPS can model an ensemble of particles...
  • HyperChem

  • Referenced in 13 articles [sw20659]
  • HyperChem is a sophisticated molecular modeling environment that is known for its quality, flexibility ... visualization and animation with quantum chemical calculations, molecular ... mechanics, and dynamics, HyperChem puts more molecular modeling tools at your fingertips than any other...
  • Cytoscape

  • Referenced in 77 articles [sw09080]
  • Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Cytoscape is an open ... with high-throughput expression data and other molecular states into a unified conceptual framework. Although ... applicable to any system of molecular components and interactions, Cytoscape is most powerful when used ... that are increasingly available for humans and model organisms. Cytoscape’s software Core provides basic...
  • Open Babel

  • Referenced in 14 articles [sw19551]
  • convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related...
  • Chaco

  • Referenced in 117 articles [sw09640]
  • computational studies including investigation of the molecular structure of liquid crystals, evaluating the design ... chemical vapor deposition reactor and modeling automobile collisions...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • unprecedented mass of molecular information for a wide range of model organisms. This provides ... begin to build models for simulating intracellular molecular processes to predict the dynamic behavior ... detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation...
  • GULP

  • Referenced in 20 articles [sw01459]
  • lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields ... within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems...
  • TINKER

  • Referenced in 10 articles [sw04095]
  • Tools for Molecular Design. The TINKER molecular modeling software is a complete and general package ... OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang’s polarizable model, and the AMOEBA ... solvation treatments including several generalized Born (GB/SA) models, generalized Kirkwood implicit solvation for AMOEBA ... symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor...
  • MAMMOTH

  • Referenced in 11 articles [sw26215]
  • MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Advances...
  • MMTK

  • Referenced in 9 articles [sw26798]
  • Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications...
  • VAMPnets

  • Referenced in 12 articles [sw32927]
  • protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transformation of simulated ... state model or related model of the interconversion rates between molecular structures. This handcrafted approach ... step will lead to large modeling errors. Here we employ the variational approach for Markov ... develop a deep learning framework for molecular kinetics using neural networks, dubbed VAMPnets. A VAMPnet...
  • STAPL

  • Referenced in 14 articles [sw00910]
  • that currently provide a SPMD model of parallelism, and supports nested parallelism. The library ... such as particle transport calculations, molecular dynamics, geometric modeling, and graph algorithms. STAPL provides several ... present results obtained using STAPL for a molecular dynamics code and a particle transport code...
  • Avogadro

  • Referenced in 6 articles [sw15099]
  • cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas...
  • Tiamat

  • Referenced in 6 articles [sw00963]
  • graphical user interface driven molecular modeling, editing and visualization tool called Tiamat. Tiamat addresses...