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BindingDB_​FMCT-Fingerprint,batch

Workflow: FMCT - Fingerprint, batchPurpose: This workflow suggests what protein Target(s) your Compound batch of interest is likely tobind, based on what Targets are bound by similar Compounds in BindingDB.Instructions: Double-click on the SDF Reader "Input batch Compounds" node and select an SD filewith one or several compounds to test. If a "duplicate row ID" error occurs, modify the SDF Readersetting and do not check the box for "use molecule name as row ID". Double-click on the Table Reader"Read clustered fingerprint data" node and select the KNIME data table generated with the BDBBuilderworkflow or with ReducedReferenceSet Table. Optionally, modify the green “Similarity Threshold” and“Affinity Cutoff” nodes with desired values. Finally, right click the Interactive Table “Predict Targets ofmy Compound” node and select “Execute and Open Views”. When the run is complete, the green lightwill turn on below this node. Right-click on it and choose “View: Table View” to see the table of similarCompounds, their similarities to your Compound, and their associated Targets. Results are limited tothe top three hits for each input compound, displayed across each row.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 CutoffRead clustered fingerprint dataInput batchCompoundsPredict Targets of my CompoundDouble Input (legacy)(deprecated) Double Input (legacy)(deprecated) Table Reader Multi-compoundComparison SDF Reader Interactive Table Workflow: FMCT - Fingerprint, batchPurpose: This workflow suggests what protein Target(s) your Compound batch of interest is likely tobind, based on what Targets are bound by similar Compounds in BindingDB.Instructions: Double-click on the SDF Reader "Input batch Compounds" node and select an SD filewith one or several compounds to test. If a "duplicate row ID" error occurs, modify the SDF Readersetting and do not check the box for "use molecule name as row ID". Double-click on the Table Reader"Read clustered fingerprint data" node and select the KNIME data table generated with the BDBBuilderworkflow or with ReducedReferenceSet Table. Optionally, modify the green “Similarity Threshold” and“Affinity Cutoff” nodes with desired values. Finally, right click the Interactive Table “Predict Targets ofmy Compound” node and select “Execute and Open Views”. When the run is complete, the green lightwill turn on below this node. Right-click on it and choose “View: Table View” to see the table of similarCompounds, their similarities to your Compound, and their associated Targets. Results are limited tothe top three hits for each input compound, displayed across each row.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 CutoffRead clustered fingerprint dataInput batchCompoundsPredict Targets of my CompoundDouble Input (legacy)(deprecated) Double Input (legacy)(deprecated) Table Reader Multi-compoundComparison SDF Reader Interactive Table

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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: 2024-04-23
Created with KNIME version: v3.7.1

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