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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


URL: Unveiling Biological Targets with KNIME - A Hands-On Workflow Powered by ChEMBL Data https://medium.com/low-code-for-advanced-data-science/unveiling-biological-targets-with-knime-96562922aeb1

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 nearest neighbours in ChEMBL
Retrieve activities from ChEMBL
WebPortal
WebPortal
WebPortal
WebPortal
WebPortal
WebPortal
WebPortal
Apply an activity threshold to select all the compounds of the reference target that are cosidered active and with which we want to build a biological targes profile.
WebPortal
WebPortal page with required interaction
WebPortal page with required interaction
WebPortal page with required interaction
WebPortal page with possible required interaction
WebPortal page with required interaction
Filters and structure manipulation
WebPortal page
WebPortal page
Export files
Display the target-ligand interaction matrix
WebPortal
WebPortal
WebPortal
WebPortal page with required interaction
WebPortal
WebPortal
Molecule input
WebPortal
WebPortal
WebPortal
WebPortal
WebPortal
WebPortal
WebPortal
WebPortal
WebPortal
WebPortal
Possible WebPortal
WebPortal page
WebPortal
select multiple moleculesinput method
Multiple Molecules Input Method Selection
large input datasetswitch end
CASE Switch End
large input datasetswitch start
CASE Switch Start
outfile_interaction_matrix_csv
CSV Writer
check whether the maximum inputdataset size is reached. In that caseit filters only the top-n moleculesand trigger a warning (n=set threshold)
Max Input Dataset Size Checker
check whether the maximum inputdataset size is reached. In that caseit filters only the top-n moleculesand trigger a warning (n=set threshold)
Max Input Dataset Size Checker
outfile_bioprofile_data_csv
CSV Writer
large_input_dataset = 1if > 1000 mols
determine if large input dataset
connect to chembl DB
ChEMBL DB Connection
calculate target-ligandinteraction matrix
ChEMBL Target-Ligand Interaction Matrix Calculation
show target-ligandinteraction matrix
ChEMBL Target-Ligand Interaction Matrix Visualization
large input datasetswitch start
CASE Switch Start
workflow intro
Text View
large input datasetswitch end
CASE Switch End
select onlymolecule col
Column Filter
extract rowIDas chembl_id
RowID
No Active Compounds Available
no active compoundsavailable switch start
Empty Table Switch
Temp File Path Generator
wait outfileto be written
Merge Variables
convert mol2 to smiles
OpenBabel
input mols as file
File Upload
SDF File Handling
Single Molecule From Text Input
show parsed moleculestructures
Query Molecules Confirmation (multi)
mol_input_methodcase switch start:0. single molecule1. multiple molecules
CASE Switch Start
CSV-SMILES File Handling
filter only Molecule col
Column Filter
filter outsimilarity col
Column Filter
retrieve single-proteinactivities
ChEMBL Activity From Molecule Retrieval
no similar compoundsavailable switch start
Empty Table Switch
mol_input_methodcase switch end
CASE Switch End
No Similar Compounds Available
Multiple Molecules Input
Text View
ChEMBL Molecule Search
parse to RDKit
RDKit From Molecule
select single ormultiple moleculeas input
Molecule Input Method Selection
mol_input_methodswitch start:0. single molecule1. multiple molecules
CASE Switch Start
generate inchi &inchikey
RDKit To InChI
missing_target_searchkeyword switch end
CASE Switch End
ChEMBL Target Search Configuration
missing_target_searchkeyword switch start
CASE Switch Start
Empty Table Switch
Uncommon Molecule Filter
missing_target_search_keywords
Rule Engine Variable
Salt Stripper
ChEMBL Activity Type Selection
outfile_formatswitch start:1. csv2. xlsx
CASE Switch Start
Cols & Vars handling
Molecule Activity Aggregation
ChEMBL Activity Type Retrieval
defineinfile_type_case
Rule Engine Variable
infile_type switch start:0. csv, tsv, xls, xlsx1. smi, smiles2. sd, sdf
CASE Switch Start
UniChem Molecule Variants Selection
no activity availableswitch start
Empty Table Switch
No Activities Available
outfile_formatswitch start:1. csv2. xlsx
CASE Switch Start
select reference targetactive compounds
Target Hits Selection
Missing Target Search Keywords
it just propagate theactive/inactive branch
Table Row to Variable
outfile_interaction_matrix_svg
Image Writer (Port)
infile_typeswitch end
CASE Switch End
outfile_active_target_profile_svg
Image Writer (Port)
show parsed moleculestructures
Query Molecules Confirmation (multi)
CSV-SMILES File Handling
ChEMBL Target Selection
multiple_mols_input_methodswitch end:0. from file1. smiles
CASE Switch End
No Target Selected
multiple_mols_input_methodswitch start:0. from file1. smiles
CASE Switch Start
input mols as file
File Upload
ChEMBL Target Search
not_found_query_molswitch start
CASE Switch Start
not_found_query_molswitch end
CASE Switch End
Select Outfile Format
display a molecule-not-foundpage
Query Molecule Not Found
not found query mol vars
Large Input Dataset
large input datasetswitch start
CASE Switch Start
tabular_infile_type
Rule Engine Variable
large input datasetswitch end
CASE Switch End
target profile methodswitch start:1. reference compound set2. reference compound NN3. reference target active compounds
CASE Switch Start
large input datasetswitch end
CASE Switch End
target profile methodswitch end
CASE Switch End
large input datasetswitch start
CASE Switch Start
infile_type switch start:0. csv, xls, xlsx1. smi, smiles2. sd, sdf3. mol2
CASE Switch Start
large input datasetswitch start
CASE Switch Start
target_profile_method
Target Profile Method Selection
large input datasetswitch end
CASE Switch End
display a molecule-not-parsedpage
Query Molecule Parsing Problems
second outport activewhen we have parsing problems
Empty Table Switch
outfile_formatswitch end
CASE Switch End
outfile_formatswitch end
CASE Switch End
interaction matrix xlsx
Excel Writer
bioprofile data xlsx
Excel Writer
render mol_struct
Renderer to Image
resort cols
Column Resorter
build & show biologicaltarget profile
ChEMBL Bioprofile Analysis
search for chembl_idsthrough unichem
UniChem Molecule Search
resort cols
Column Resorter
render mol_struct
Renderer to Image
No Activity Type Selected
ChEMBL Activity Retrieval
switch bottom ifno activity is retrieved
Empty Table Switch
copy/paste multiple smiles
Multiple Molecules Input
filter out rows withmissing inchikey
Row Filter (deprecated)
Molecule Structure Sketcher
single molecule inputmethod switch end
CASE Switch End
second outport activewhen we have parsing problemswith all the molecules
Empty Table Switch
select single moleculeinput method
Single Molecule Input Method Selection
display a molecule-not-parsedpage
Query Molecule Parsing Problems
multiple_mols_input_methodswitch end:0. from file1. smiles
CASE Switch End
mol_input_methodswitch end
CASE Switch End
select multiple moleculesinput method
Multiple Molecules Input Method Selection
single molecule inputmethod switch start
CASE Switch Start
selectsearched_compound
Column Filter
extractsearched_mol_id
RowID
to smiles
RDKit To Molecule
multiple_mols_input_methodswitch start:0. from file1. smiles
CASE Switch Start
infile_typeswitch end
CASE Switch End
Nearest Neighbours Selection
select searched_mol_id,searched_compound & chembl_id
Column Filter
rename
Column Rename (deprecated)
filter out rows withmissing inchikey
Row Filter (deprecated)
select cols
Column Filter
parse to RDKit
RDKit From Molecule
try to retrieve name &synonyms from chembl
chembl inchikey to name
use chembl_id as molID/rowID
download outputfiles
Download Output Files
SDF File Handling
Query Molecule Confirmation (single)
generate inchi &inchikey
RDKit To InChI
select queryinchikey
Column Filter

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: 2026-01-21
Created with KNIME version: v5.8.1
Tags: data introspectiondata retrievalligand-basedtarget-based

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