• IntAct

  • Referenced in 24 articles [sw21665]
  • IntAct:an open source molecular interaction database. IntAct provides an open source database and toolkit...
  • KEGG

  • Referenced in 239 articles [sw13866]
  • Genes and Genomes. KEGG is a database resource for understanding high-level functions and utilities ... molecular-level information. It is a computer representation of the biological system, consisting of molecular ... integrated with the knowledge on molecular wiring diagrams of interaction, reaction and relation networks (systems...
  • Cytoscape

  • Referenced in 59 articles [sw09080]
  • molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases ... protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model ... phenotypes, and other molecular states; and to link the network to databases of functional annotations ... surveyed, including a search for interaction pathways correlating with changes in gene expression, a study...
  • QNet

  • Referenced in 9 articles [sw13845]
  • Tool for Querying Protein Interaction Networks. Molecular interaction databases can be used to study ... known yeast complexes against a fly protein interaction network. This comparison points to strong conservation...
  • HITEMP

  • Referenced in 7 articles [sw28455]
  • called HITEMP, is analogous to the HITRAN database but encompasses many more bands and transitions ... local thermodynamic equilibrium problems, and investigating molecular interactions, to name a few. The sources...
  • DrugBank

  • Referenced in 8 articles [sw23876]
  • docking or screening, drug metabolism prediction, drug interaction prediction and general pharmaceutical education. The latest ... data has also been added to the database, with the latest version of DrugBank containing ... molecular biological data. A number of new data fields, including food–drug interactions, drug–drug...
  • UniHI

  • Referenced in 2 articles [sw17425]
  • interaction maps have become important tools of biomedical research for the elucidation of molecular mechanisms ... disease processes. The Unified Human Interactome database (UniHI, http://www.unihi.org) provides researchers with a comprehensive ... query and access human protein–protein interaction (PPI) data. Since its first release, UniHI...
  • iPfam

  • Referenced in 1 article [sw29349]
  • Bank. The database iPfam, available at http://ipfam.org, catalogues Pfam domain interactions based on known ... molecular level. Previously, the iPfam domain–domain interaction data was integrated within the Pfam database...
  • InnateDB

  • Referenced in 1 article [sw29345]
  • database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions...
  • Onto-Tools

  • Referenced in 10 articles [sw10974]
  • four seamlessly integrated databases: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Onto-Express ... function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values ... relevant biological processes, specific mechanisms of interactions can be hypothesized for the conditions studied. Currently...
  • MatrixDB

  • Referenced in 1 article [sw29346]
  • matrixdb.ibcp.fr) is a freely available database focused on interactions established by extracellular proteins and polysaccharides ... active member of the International Molecular Exchange (IMEx) consortium and has adopted ... standards for annotating and exchanging interaction data, either at the MIMIx or IMEx level. MatrixDB ... importing extracellular interaction data from other IMEx databases. Other major changes include the creation...
  • SNPs3D

  • Referenced in 5 articles [sw30035]
  • relevant. We describe a web resource and database that provides and integrates as much information ... possible on disease/gene relationships at the molecular level. Description: The resource http://www.SNPs3D.org has three ... mouse knockout information and papers. Gene-gene interactions are presented in an interactive graphical interface...
  • LUDI

  • Referenced in 1 article [sw24443]
  • Cambridge Structural Database. An alternative route to generate the interaction sites ... second step is the fit of molecular fragments onto the interaction sites. Currently...
  • StSNP

  • Referenced in 3 articles [sw30039]
  • protein, alone or in the interactions in a multi-protein complex, by increasing/decreasing the activity ... such changes and drawing conclusions about the molecular basis of diseases, involves integrating information from ... proteins. The data from NCBI’s SNP database (dbSNP), gene and protein databases from Entrez...
  • DockingApp

  • Referenced in 2 articles [sw27816]
  • structural and energetic bases of the interaction between macromolecules and substrates, endogenous and exogenous ligands ... users to exploit the full potential of molecular docking. Along this path, here is described ... screening and drug repurposing initiatives. Furthermore, other databases of compounds such as ZINC, available also...
  • hiPathDB

  • Referenced in 1 article [sw25646]
  • systematic organization and integration of complex interactions taking place within various biological pathways. Currently ... multiple databases in various formats. hiPathDB is an integrated pathway database that combines the curated ... model that takes distinct features of four databases into account and subsequently reformatting all pathways ... merging common components. Even though the detailed molecular-level information such as complex formation...
  • GAP

  • Referenced in 2702 articles [sw00320]
  • GAP is a system for computational discrete algebra...
  • Maple

  • Referenced in 4919 articles [sw00545]
  • The result of over 30 years of cutting...
  • Mathematica

  • Referenced in 5703 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 11496 articles [sw00558]
  • MATLAB® is a high-level language and interactive...