• Cytoscape

  • Referenced in 76 articles [sw09080]
  • Software Environment for Integrated Models of Biomolecular Interaction Networks. Cytoscape is an open source software ... project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states...
  • MVPoisson

  • Referenced in 4 articles [sw18574]
  • application areas, such as queuing and biomolecular networks. This note shows how to compute conditional ... made freely available. A discussion of motivating biomolecular problems is also provided...
  • SloppyCell

  • Referenced in 3 articles [sw13614]
  • environment for simulation and analysis of biomolecular networks. Features: support for much of the Systems...
  • CytoCtrlAnalyser

  • Referenced in 1 article [sw34201]
  • CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis. Studying the controllability of biomolecular networks ... platform for analyzing controllability of biomolecular networks although various algorithms for analyzing complex network controllability ... comprehensive platform for analyzing controllability of biomolecular networks. Nine algorithms have been integrated in CytoCtrlAnalyser ... targets or biologically important nodes in biomolecular networks. Availability and implementation: Freely available for downloading...
  • REACH

  • Referenced in 6 articles [sw00788]
  • biomolecular simulation. The program calculates the force constants of a residue-scale elastic network model...
  • BisoGenet

  • Referenced in 2 articles [sw35192]
  • BisoGenet: a new tool for gene network building, visualization and analysis. Results: BisoGenet ... tier application for visualization and analysis of biomolecular relationships. The system consists of three tiers ... pathways. In the middle tier, a global network is created at server startup, representing...
  • VAMPnets

  • Referenced in 11 articles [sw32927]
  • structures, equilibria and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from ... learning framework for molecular kinetics using neural networks, dubbed VAMPnets. A VAMPnet encodes the entire...
  • MOLE

  • Referenced in 2 articles [sw18622]
  • mesh. Tests on a wide variety of biomolecular systems including gramicidine, acetylcholinesterase, cytochromes P450, potassium ... tool for exploring large molecular channels, complex networks of channels, and molecular dynamics trajectories...
  • Spatkin

  • Referenced in 1 article [sw34203]
  • method, which avoids enumeration of the reaction network implied by a set of rules. Models ... biomolecules. The tool is capable of simulating biomolecular interactions occurring...
  • BEMLIB

  • Referenced in 101 articles [sw00005]
  • BEMLIB is a boundary-element software library of...
  • Matlab

  • Referenced in 12640 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • TNPACK

  • Referenced in 42 articles [sw00970]
  • We present a FORTRAN package of subprograms for...
  • AMBER

  • Referenced in 56 articles [sw01333]
  • AmberTools is a set of programs for biomolecular...
  • DSSZ-MC

  • Referenced in 6 articles [sw01360]
  • DSSZ-MC -- a tool for symbolic analysis of...
  • FreeFem++

  • Referenced in 1135 articles [sw01436]
  • FreeFem++ is an implementation of a language dedicated...
  • BioGRID

  • Referenced in 8 articles [sw01699]
  • The Bio GRID developed an access portal for...
  • NAMD

  • Referenced in 78 articles [sw03198]
  • NAMD is a parallel molecular dynamics code designed...
  • CUDA

  • Referenced in 1230 articles [sw03258]
  • The NVIDIA® CUDA® Toolkit provides a comprehensive development...
  • SeDuMi

  • Referenced in 1216 articles [sw04002]
  • SeDuMi is a Matlab toolbox for solving optimization...
  • PETSc

  • Referenced in 1228 articles [sw04012]
  • The Portable, Extensible Toolkit for Scientific Computation (PETSc...