• KEGG

  • Referenced in 275 articles [sw13866]
  • knowledge on molecular wiring diagrams of interaction, reaction and relation networks (systems information). It also...
  • Cytoscape

  • Referenced in 82 articles [sw09080]
  • integrating biomolecular interaction networks with high-throughput expression data and other molecular states into ... framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful ... basic functionality to layout and query the network; to visually integrate the network with expression ... profiles, phenotypes, and other molecular states; and to link the network to databases of functional...
  • BioNetGen

  • Referenced in 60 articles [sw09072]
  • signal transduction based on the interactions of molecular domains. BioNetGen allows a user to create ... output defines and parameterizes the network of molecular species that can arise during signaling...
  • MCODE

  • Referenced in 49 articles [sw35748]
  • automated method for finding molecular complexes in large protein interaction networks. Results: This paper describes ... large protein-protein interaction networks that may represent molecular complexes. The method is based ... interest without considering the rest of the network and allows examination of cluster interconnectivity, which...
  • PORGY

  • Referenced in 14 articles [sw06923]
  • such as the evolution of bio-molecular networks, adhoc communication networks or interaction nets...
  • QNet

  • Referenced in 11 articles [sw13845]
  • Tool for Querying Protein Interaction Networks. Molecular interaction databases can be used to study ... evolution of molecular pathways across species. Querying such pathways is a challenging computational problem ... limited to simple queries (paths), or simple networks (forests). In this paper, we significantly extend...
  • VAMPnets

  • Referenced in 19 articles [sw32927]
  • deep learning framework for molecular kinetics using neural networks, dubbed VAMPnets. A VAMPnet encodes...
  • ARACNE

  • Referenced in 38 articles [sw17200]
  • identifying direct transcriptional interactions in mammalian cellular networks, a problem that has challenged existing reverse ... identify molecular targets of pharmacological compounds in mammalian cellular networks...
  • Polynome

  • Referenced in 6 articles [sw12584]
  • long been used as models of molecular networks, and they play an increasingly important role...
  • iCDI-PseFpt

  • Referenced in 15 articles [sw30067]
  • channel-drug interaction in cellular networking with PseAAC and molecular fingerprints. Many crucial functions ... study of ion channel-drug interaction networks is an important topic for drug development. However ... interacting with each other in a cellular network by means of experimental techniques. Although some ... theory, the drug compound by the 2D molecular fingerprint, and the operation engine...
  • DINGO

  • Referenced in 4 articles [sw29317]
  • DINGO: differential network analysis in genomics. Motivation: Cancer progression and development ... initiated by aberrations in various molecular networks through coordinated changes across multiple genes and pathways...
  • StochPy

  • Referenced in 7 articles [sw27252]
  • package for stochastic simulation of the molecular control networks of living cells. It allows novice...
  • GeneWays

  • Referenced in 4 articles [sw23128]
  • infer a consensus view of molecular networks. GeneWays is designed as an open platform, allowing...
  • DyNetViewer

  • Referenced in 2 articles [sw24787]
  • dynamic network construction, analysis and visualization. SUMMARY: The molecular interactions in a cell are varying ... construction and analysis of dynamic molecular networks can elucidate dynamic cellular mechanisms of different biological...
  • IGLOO

  • Referenced in 2 articles [sw14829]
  • find regions of similarities between molecular networks of different species. NA can be either local...
  • multistatepdscontrol

  • Referenced in 2 articles [sw31987]
  • Control of intracellular molecular networks using algebraic methods. Many problems in biology and medicine have...
  • MOLE

  • Referenced in 3 articles [sw18622]
  • powerful tool for exploring large molecular channels, complex networks of channels, and molecular dynamics trajectories...
  • SQUAD

  • Referenced in 5 articles [sw29353]
  • Qualitative Modeling of Regulatory Networks. The wealth of molecular information provided by high-throughput technologies ... efforts dedicated to the reconstruction of regulatory networks in diverse biological systems. This information, however...
  • GRID Infoware

  • Referenced in 23 articles [sw04166]
  • compute and data intensive computing applications (e.g, molecular modelling for drug design, brain activity analysis ... This idea is analogous to electric power network (grid) where power generators are distributed...
  • TopoGSA

  • Referenced in 2 articles [sw30015]
  • gene and protein sets in molecular interaction networks. Different topological characteristics, such as the centrality...