iPHACE
integrative navigation in pharmacological space
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Filtering options

This working area allows the user to search or filter the iPHACE contents. A brief description of the three tabs of this area follows:

  • Text Search: enter a term to search a complete thesaurus of drug and target names and synonims and check whether interaction data exists currently in iPHACE. Four different results are possible:
    • the term is identified in the thesaurus and interaction data is present in iPHACE: if the term is identified as a drug, clicking on the drug name will display the Drug card; if the term is identified as a target, clicking on the target name will reload iPHACE to update all working areas with the information related to that target
    • the term is recognised in the thesaurus as a drug but no interaction data is present in iPHACE: in this case, the message that will appear will be "No interactions with GPCR and/or ion channel targets were found for drug in All DBs", drug in this phrase being the term entered
    • the term is recognised in the thesaurus as a target but no interaction data is present in iPHACE: in this case, the message that will appear will be "No interactions with drugs were found for target in All DBs", target in this phrase being the term entered
    • the term is not recognised in the thesaurus: in this case, the message that will appear will be "The term term was not recognized neither as drug nor as GPCR or ion channel target in the current thesaurus", term in this phrase being the term entered

  • Substructure Search: by clicking on this tab, chemaxon's MarvinSketch applet will be loaded and a light-grey rectangle will then appear. Click on the rectangle and the drawing applet will appear. You may then draw a structure and when closing the applet that structure will be shown inside the light-grey rectangle. Finally, click on the search icon and all working areas will be updated with the information corresponding to those drugs containing the substructure drawn. The filtering is performed with the substructure search algorithm available from chemaxon.

  • Filters: by clicking on this tab, four different filters can be applied to the iPHACE contents. Filters can be combined and will also be applied to any Text search or Substructure search. Selecting the checkbox next to certain filter will make it active and pressing the apply filtering button all active filters will be applied. A brief description of each filter follows:
    • Profile Filtering: this feature allows the user to search for ligands with similar activity profiles. First thing to do is to choose a molecule or list of molecules to be the reference of our search. This can be done by clicking on the profile search checkboxes present either in the Structural browser or in the Drug chart. Then, one needs to specify a level of profile similarity above which drugs will be kept: default value is set to 0.6. The similarity between the activity profiles of two drugs having affinity for N targets is obtained by computing the Euclidean distance between the respective affinity vectors relative to the maximum Euclidean distance found for a pair of drugs in the set having affinity for N targets.
    • Affinity Filtering: keeps only drugs containing interactions with the specified type, selected from a drop-down menu.
    • Promiscuity Filtering: keeps only drugs that contain interaction data above/below a given value entered by the user.
    • Species Filtering: keeps only drugs containing interactions with targets from a given species, selected from a drop-down menu.

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