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BindingDB_​FMCT-Fingerprint

Workflow: FMCT - FingerprintPurpose: This workflow suggests what protein Target(s) your Compound of interest is likely to bind,based on what Targets are bound by similar Compounds in BindingDB.Instructions: Double-click on the MarvinSketch “Input Compound” node and use the resultingwindow to draw, paste or open a file with your small molecule of interest. Double-click on the TableReader "Read fingerprint data" node and select the KNIME data table generated with the BDBBuilderworkflow. Optionally, modify the green “Similarity Threshold” and “Affinity Cutoff” nodes with desiredvalues. Finally, right click the MarvinVew “Predict Targets of my Compound” node and select “Executeand Open Views”. When the run is complete, the green light will turn on below this node. Right-clickon it and choose “View: MarvinView” to see the table of similar Compounds, their similarities to yourCompound, and their associated Targets. If you found too many results, you may want to use a higher(more stringent) compound similarity threshold, or a lower (more stringent) affinity (e.g. Ki) cutoff. Toincrease the font size in the MarvinView table, use Table-->Options--> Font Size.This workflow computes a chemical fingerprint of your Compound and compares it with storedchemical fingerprints for Compounds in BindingDB. It selects Compounds that are similar to yourCompound, based on the Similarity Threshold, and checks whether they bind a Target with an affinityexceeding (tighter binding) the selected Affinity Cutoff. Those Compounds meeting both criteria aredisplayed, along with their associated Targets and binding affinities. Similarity ThresholdAffinity CutoffPredict Targets of my CompoundRead fingerprintdataInput CompoundDouble Input (legacy)(deprecated) Double Input (legacy)(deprecated) Comparisons MarvinView Table Reader MarvinSketch Workflow: FMCT - FingerprintPurpose: This workflow suggests what protein Target(s) your Compound of interest is likely to bind,based on what Targets are bound by similar Compounds in BindingDB.Instructions: Double-click on the MarvinSketch “Input Compound” node and use the resultingwindow to draw, paste or open a file with your small molecule of interest. Double-click on the TableReader "Read fingerprint data" node and select the KNIME data table generated with the BDBBuilderworkflow. Optionally, modify the green “Similarity Threshold” and “Affinity Cutoff” nodes with desiredvalues. Finally, right click the MarvinVew “Predict Targets of my Compound” node and select “Executeand Open Views”. When the run is complete, the green light will turn on below this node. Right-clickon it and choose “View: MarvinView” to see the table of similar Compounds, their similarities to yourCompound, and their associated Targets. If you found too many results, you may want to use a higher(more stringent) compound similarity threshold, or a lower (more stringent) affinity (e.g. Ki) cutoff. Toincrease the font size in the MarvinView table, use Table-->Options--> Font Size.This workflow computes a chemical fingerprint of your Compound and compares it with storedchemical fingerprints for Compounds in BindingDB. It selects Compounds that are similar to yourCompound, based on the Similarity Threshold, and checks whether they bind a Target with an affinityexceeding (tighter binding) the selected Affinity Cutoff. Those Compounds meeting both criteria aredisplayed, along with their associated Targets and binding affinities. Similarity ThresholdAffinity CutoffPredict Targets of my CompoundRead fingerprintdataInput CompoundDouble Input (legacy)(deprecated) Double Input (legacy)(deprecated) Comparisons MarvinView Table Reader MarvinSketch

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: Preferred Customer
Created at: 2014-08-28
On NodePit since: 2019-07-12
Last update: 2024-04-17
Created with KNIME version: v3.7.1

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