Icon

Biological Target Profile

This workflow leverages the ChEMBL database to obtain target profiles for different compound sets, focusing specifically on single-protein targets. It is designed for various applications, including on- and off-target deconvolution, data introspection, and biological profile determination.

To begin, you select the compound set for which you wish to construct a target profile. The workflow then verifies the presence of these compounds in the ChEMBL database, retrieving all concentration-response activities associated with single-protein targets. The activity types currently supported include: IC50, EC50, XC50, AC50, Ki, Kd, and potency. Using this data, a comprehensive target-ligand interaction matrix is generated. Each target-ligand activity identified is reported along with its data source, such as a reference to the original publication and DOI. Additionally, the workflow offers a user-adjustable activity threshold to help create an active targets profile specific to the compound set.

Currently, target profiles can be generated from the following compound sets:

1. A user-defined compound set
2. Structurally similar molecules of one (or a few) reference compound(s) (AKA reference compound nearest neighbors)
3. Compounds that interact with a reference target

Reference target active compounds profile Reference compound nearest neighbours profile Multiple molecules input Reference compounds profile Multiple molecules input Display biologic profiles Filter by similarity WebPortal WebPortal WebPortal WebPortal WebPortal Generate and select inchikey Search UniChem Display a warning page if query molecule is not found. UniChem molecule variant selection Try to retrieve molecule name & synonyms and ask the user to confirm the parsed molecular structure WebPortal WebPortal Generate and select inchikey Search reference compound nearestneighbours in ChEMBL Retrieve activities from ChEMBL WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal Apply an activity threshold to selectall the compounds of the referencetarget that are cosidered active andwith which we want to build abiological targes profile. WebPortal WebPortal page withrequired interaction WebPortal page withrequired interaction WebPortal page withrequired interaction WebPortal page withpossible required interaction WebPortal page withrequired interaction Filters and structure manipulation WebPortal page WebPortal page Export files Display the target-ligand interaction matrix WebPortal WebPortal WebPortal WebPortal page withrequired interaction WebPortal WebPortal Molecule input WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal Possible WebPortal WebPortal page WebPortal parse to RDKitselect single ormultiple moleculeas inputmol_input_methodswitch start:0. single molecule1. multiple moleculesgenerate inchi &inchikeyselect queryinchikeydefineinfile_type_caseinfile_type switch start:0. csv, tsv, xls, xlsx1. smi, smiles2. sd, sdfinfile_typeswitch endmultiple_mols_input_methodswitch start:0. from file1. smilesinput mols as filemultiple_mols_input_methodswitch end:0. from file1. smilesnot_found_query_molswitch startnot_found_query_molswitch enddisplay a molecule-not-foundpageshow parsed moleculestructuresdownload outputfilesoutfile_formatswitch start:1. csv2. xlsxsearch for chembl_idsthrough unichemdisplay a molecule-not-parsedpagesecond outport activewhen we have parsing problemstabular_infile_typeinfile_type switch start:0. csv, xls, xlsx1. smi, smiles2. sd, sdf3. mol2target_profile_methodtarget profile methodswitch start:1. reference compound set2. reference compound NN3. reference target active compoundstarget profile methodswitch endfilter out rows withmissing inchikeyselect searched_mol_id,searched_compound & chembl_idrenameselect colsparse to RDKittry to retrieve name &synonyms from chemblgenerate inchi &inchikeysecond outport activewhen we have parsing problemswith all the moleculesdisplay a molecule-not-parsedpagefilter out rows withmissing inchikeyto smilesselectsearched_compoundextractsearched_mol_idfilter outsimilarity colretrieve single-proteinactivitiesno similar compoundsavailable switch startoutfile_interaction_matrix_csvoutfile_bioprofile_data_csvwait outfileto be writtenno active compoundsavailable switch startselect onlymolecule colextract rowIDas chembl_idoutfile_active_target_profile_svgoutfile_interaction_matrix_svgswitch bottom ifno activity is retrievedmissing_target_searchkeyword switch startmissing_target_searchkeyword switch endmissing_target_search_keywordsoutfile_formatswitch start:1. csv2. xlsxinteraction matrix xlsxoutfile_formatswitch endoutfile_formatswitch endbioprofile data xlsxrender mol_structresort colsresort colsrender mol_structbuild & show biologicaltarget profilelarge input datasetswitch startlarge input datasetswitch endlarge input datasetswitch startlarge input datasetswitch endlarge input datasetswitch endlarge input datasetswitch startcheck whether the maximum inputdataset size is reached. In that caseit filters only the top-n moleculesand trigger a warning (n=set threshold)large_input_dataset = 1if > 1000 molslarge input datasetswitch endlarge input datasetswitch startlarge input datasetswitch startlarge input datasetswitch endcalculate target-ligandinteraction matrixshow target-ligandinteraction matrixselect reference targetactive compoundsno activity availableswitch startit just propagate theactive/inactive branchselect single moleculeinput methodmultiple_mols_input_methodswitch end:0. from file1. smilessingle molecule inputmethod switch endsingle molecule inputmethod switch startmol_input_methodswitch endselect multiple moleculesinput methodcopy/paste multiple smilesmultiple_mols_input_methodswitch start:0. from file1. smilesinfile_typeswitch endconvert mol2 to smilesinput mols as filefilter only Molecule colshow parsed moleculestructuresmol_input_methodcase switch start:0. single molecule1. multiple moleculesmol_input_methodcase switch endcheck whether the maximum inputdataset size is reached. In that caseit filters only the top-n moleculesand trigger a warning (n=set threshold)connect to chembl DBworkflow introselect multiple moleculesinput method ChEMBL MoleculeSearch RDKit From Molecule Molecule InputMethod Selection CASE Switch Start RDKit To InChI Column Filter Rule EngineVariable CASE Switch Start CASE Switch End CASE Switch Start File Upload CSV-SMILESFile Handling CASE Switch End CASE Switch Start CASE Switch End Query MoleculeNot Found not found querymol vars MultipleMolecules Input Query MoleculesConfirmation (multi) use chembl_idas molID/rowID UniChem MoleculeVariants Selection DownloadOutput Files CASE Switch Start UniChemMolecule Search Query MoleculeParsing Problems Empty Table Switch Select OutfileFormat Rule EngineVariable CASE Switch Start Target ProfileMethod Selection CASE Switch Start CASE Switch End Row Filter Column Filter Column Rename(deprecated) Column Filter RDKit From Molecule chembl inchikeyto name Query MoleculeConfirmation (single) RDKit To InChI Empty Table Switch Query MoleculeParsing Problems Row Filter RDKit To Molecule Column Filter RowID Nearest NeighboursSelection Column Filter ChEMBL Activity FromMolecule Retrieval Empty Table Switch No Similar CompoundsAvailable CSV Writer CSV Writer Merge Variables No Active CompoundsAvailable Empty Table Switch Column Filter RowID Image Writer (Port) Image Writer (Port) ChEMBL TargetSearch ChEMBL TargetSelection ChEMBL ActivityType Retrieval ChEMBL ActivityType Selection Empty Table Switch No ActivityType Selected ChEMBL ActivityRetrieval Missing TargetSearch Keywords No Target Selected CASE Switch Start Empty Table Switch CASE Switch End ChEMBL Target SearchConfiguration Rule EngineVariable Salt Stripper UncommonMolecule Filter Cols & Varshandling Molecule ActivityAggregation CASE Switch Start Excel Writer CASE Switch End CASE Switch End Excel Writer Renderer to Image Column Resorter Column Resorter Renderer to Image ChEMBL BioprofileAnalysis Large Input Dataset CASE Switch Start CASE Switch End CASE Switch Start CASE Switch End CASE Switch End CASE Switch Start Max Input DatasetSize Checker determine if largeinput dataset CASE Switch End CASE Switch Start CASE Switch Start CASE Switch End ChEMBL Target-LigandInteraction Matrix Calculation ChEMBL Target-Ligand InteractionMatrix Visualization Target HitsSelection Empty Table Switch No ActivitiesAvailable Table Rowto Variable SDF File Handling Single Molecule InputMethod Selection CASE Switch End Molecule StructureSketcher CASE Switch End CASE Switch Start CASE Switch End Multiple MoleculesInput Method Selection MultipleMolecules Input CASE Switch Start CASE Switch End SDF File Handling Single MoleculeFrom Text Input OpenBabel File Upload CSV-SMILESFile Handling Column Filter Query MoleculesConfirmation (multi) CASE Switch Start CASE Switch End Max Input DatasetSize Checker ChEMBL DBConnection Text View Text View Multiple MoleculesInput Method Selection Temp File PathGenerator Reference target active compounds profile Reference compound nearest neighbours profile Multiple molecules input Reference compounds profile Multiple molecules input Display biologic profiles Filter by similarity WebPortal WebPortal WebPortal WebPortal WebPortal Generate and select inchikey Search UniChem Display a warning page if query molecule is not found. UniChem molecule variant selection Try to retrieve molecule name & synonyms and ask the user to confirm the parsed molecular structure WebPortal WebPortal Generate and select inchikey Search reference compound nearestneighbours in ChEMBL Retrieve activities from ChEMBL WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal Apply an activity threshold to selectall the compounds of the referencetarget that are cosidered active andwith which we want to build abiological targes profile. WebPortal WebPortal page withrequired interaction WebPortal page withrequired interaction WebPortal page withrequired interaction WebPortal page withpossible required interaction WebPortal page withrequired interaction Filters and structure manipulation WebPortal page WebPortal page Export files Display the target-ligand interaction matrix WebPortal WebPortal WebPortal WebPortal page withrequired interaction WebPortal WebPortal Molecule input WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal WebPortal Possible WebPortal WebPortal page WebPortal parse to RDKitselect single ormultiple moleculeas inputmol_input_methodswitch start:0. single molecule1. multiple moleculesgenerate inchi &inchikeyselect queryinchikeydefineinfile_type_caseinfile_type switch start:0. csv, tsv, xls, xlsx1. smi, smiles2. sd, sdfinfile_typeswitch endmultiple_mols_input_methodswitch start:0. from file1. smilesinput mols as filemultiple_mols_input_methodswitch end:0. from file1. smilesnot_found_query_molswitch startnot_found_query_molswitch enddisplay a molecule-not-foundpageshow parsed moleculestructuresdownload outputfilesoutfile_formatswitch start:1. csv2. xlsxsearch for chembl_idsthrough unichemdisplay a molecule-not-parsedpagesecond outport activewhen we have parsing problemstabular_infile_typeinfile_type switch start:0. csv, xls, xlsx1. smi, smiles2. sd, sdf3. mol2target_profile_methodtarget profile methodswitch start:1. reference compound set2. reference compound NN3. reference target active compoundstarget profile methodswitch endfilter out rows withmissing inchikeyselect searched_mol_id,searched_compound & chembl_idrenameselect colsparse to RDKittry to retrieve name &synonyms from chemblgenerate inchi &inchikeysecond outport activewhen we have parsing problemswith all the moleculesdisplay a molecule-not-parsedpagefilter out rows withmissing inchikeyto smilesselectsearched_compoundextractsearched_mol_idfilter outsimilarity colretrieve single-proteinactivitiesno similar compoundsavailable switch startoutfile_interaction_matrix_csvoutfile_bioprofile_data_csvwait outfileto be writtenno active compoundsavailable switch startselect onlymolecule colextract rowIDas chembl_idoutfile_active_target_profile_svgoutfile_interaction_matrix_svgswitch bottom ifno activity is retrievedmissing_target_searchkeyword switch startmissing_target_searchkeyword switch endmissing_target_search_keywordsoutfile_formatswitch start:1. csv2. xlsxinteraction matrix xlsxoutfile_formatswitch endoutfile_formatswitch endbioprofile data xlsxrender mol_structresort colsresort colsrender mol_structbuild & show biologicaltarget profilelarge input datasetswitch startlarge input datasetswitch endlarge input datasetswitch startlarge input datasetswitch endlarge input datasetswitch endlarge input datasetswitch startcheck whether the maximum inputdataset size is reached. In that caseit filters only the top-n moleculesand trigger a warning (n=set threshold)large_input_dataset = 1if > 1000 molslarge input datasetswitch endlarge input datasetswitch startlarge input datasetswitch startlarge input datasetswitch endcalculate target-ligandinteraction matrixshow target-ligandinteraction matrixselect reference targetactive compoundsno activity availableswitch startit just propagate theactive/inactive branchselect single moleculeinput methodmultiple_mols_input_methodswitch end:0. from file1. smilessingle molecule inputmethod switch endsingle molecule inputmethod switch startmol_input_methodswitch endselect multiple moleculesinput methodcopy/paste multiple smilesmultiple_mols_input_methodswitch start:0. from file1. smilesinfile_typeswitch endconvert mol2 to smilesinput mols as filefilter only Molecule colshow parsed moleculestructuresmol_input_methodcase switch start:0. single molecule1. multiple moleculesmol_input_methodcase switch endcheck whether the maximum inputdataset size is reached. In that caseit filters only the top-n moleculesand trigger a warning (n=set threshold)connect to chembl DBworkflow introselect multiple moleculesinput method ChEMBL MoleculeSearch RDKit From Molecule Molecule InputMethod Selection CASE Switch Start RDKit To InChI Column Filter Rule EngineVariable CASE Switch Start CASE Switch End CASE Switch Start File Upload CSV-SMILESFile Handling CASE Switch End CASE Switch Start CASE Switch End Query MoleculeNot Found not found querymol vars MultipleMolecules Input Query MoleculesConfirmation (multi) use chembl_idas molID/rowID UniChem MoleculeVariants Selection DownloadOutput Files CASE Switch Start UniChemMolecule Search Query MoleculeParsing Problems Empty Table Switch Select OutfileFormat Rule EngineVariable CASE Switch Start Target ProfileMethod Selection CASE Switch Start CASE Switch End Row Filter Column Filter Column Rename(deprecated) Column Filter RDKit From Molecule chembl inchikeyto name Query MoleculeConfirmation (single) RDKit To InChI Empty Table Switch Query MoleculeParsing Problems Row Filter RDKit To Molecule Column Filter RowID Nearest NeighboursSelection Column Filter ChEMBL Activity FromMolecule Retrieval Empty Table Switch No Similar CompoundsAvailable CSV Writer CSV Writer Merge Variables No Active CompoundsAvailable Empty Table Switch Column Filter RowID Image Writer (Port) Image Writer (Port) ChEMBL TargetSearch ChEMBL TargetSelection ChEMBL ActivityType Retrieval ChEMBL ActivityType Selection Empty Table Switch No ActivityType Selected ChEMBL ActivityRetrieval Missing TargetSearch Keywords No Target Selected CASE Switch Start Empty Table Switch CASE Switch End ChEMBL Target SearchConfiguration Rule EngineVariable Salt Stripper UncommonMolecule Filter Cols & Varshandling Molecule ActivityAggregation CASE Switch Start Excel Writer CASE Switch End CASE Switch End Excel Writer Renderer to Image Column Resorter Column Resorter Renderer to Image ChEMBL BioprofileAnalysis Large Input Dataset CASE Switch Start CASE Switch End CASE Switch Start CASE Switch End CASE Switch End CASE Switch Start Max Input DatasetSize Checker determine if largeinput dataset CASE Switch End CASE Switch Start CASE Switch Start CASE Switch End ChEMBL Target-LigandInteraction Matrix Calculation ChEMBL Target-Ligand InteractionMatrix Visualization Target HitsSelection Empty Table Switch No ActivitiesAvailable Table Rowto Variable SDF File Handling Single Molecule InputMethod Selection CASE Switch End Molecule StructureSketcher CASE Switch End CASE Switch Start CASE Switch End Multiple MoleculesInput Method Selection MultipleMolecules Input CASE Switch Start CASE Switch End SDF File Handling Single MoleculeFrom Text Input OpenBabel File Upload CSV-SMILESFile Handling Column Filter Query MoleculesConfirmation (multi) CASE Switch Start CASE Switch End Max Input DatasetSize Checker ChEMBL DBConnection Text View Text View Multiple MoleculesInput Method Selection Temp File PathGenerator

Nodes

Extensions

Links

Download

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

Download Workflow
Created by: giovannicincilla
Created at: 2023-04-04
On NodePit since: 2025-06-08
Last update: 2025-06-08
Created with KNIME version: v5.2.6
Tags: data introspectiondata retrievalligand-basedtarget-based

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!