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Target-Driven Bioactivity and Molecular Series Explorer

This workflow enables the retrieval and exploration of bioactivity data from ChEMBL. Given a biological target of interest, the workflow retrieves the associated compounds and their activities, applies a series of data processing steps to maximise data quality, and optionally organises the compounds into molecular series to enable a structured exploration of structure-activity relationships.

The workflow supports a broad range of target types, including single proteins, protein complexes and cell lines, and offers flexible options for molecular series identification, from scaffold-based grouping to clustering-based methods. Designed to be run either as a DataApp on a KNIME Hub instance or locally via KNIME Analytics Platform, it provides an intuitive and interactive web-based interface throughout.

For a detailed description of the workflow and its components, please refer to: https://medium.com/low-code-for-advanced-data-science/target-to-molecular-series-knime-workflow-e147a4f57e89

URL: From Target to Molecular Series: Introducing the Target-Driven Bioactivity and Molecular Series Explorer https://medium.com/low-code-for-advanced-data-science/target-to-molecular-series-knime-workflow-e147a4f57e89

Activity aggregation
Activity set selection and retrieval
Target search and selection
Optional molecular series identification
Molecular series identification and activity retrieval for selected series
Molecular structure manipulation and filtering
WebPortal page with required interaction
WebPortal page with required interaction
Web Portal page (interaction required)
Web Portal page (data-dependent)
Activity data retrieval for all molecules (aggregated and individual)
WebPortal
Molecular series identification
Web Portal page (data-dependent)
Web Portal page (interaction required)
Web Portal page (interaction required)
Web Portal page (interaction required)
Web Portal page (interaction required)
Web Portal page (interaction required)
Web Portal page (interaction required)
Web Portal page (interaction required)
Web Portal page
Web Portal page
Web Portal page
Web Portal page
Web Portal page
Web Portal page (data-dependent)
SET UP
Molecular Series Analysis & Selection
Missing Target Search Keywords
Uncommon Molecule Filter
ChEMBL Target Selection
ChEMBL DB connection setup
ChEMBL DB Connection
sort molactivity desc
Sorter
selected mol series switch starttrigger a message if nomol series is selected
Empty Table Switch
identify_mol_seriesswitch start1. all mols individually2. identify mol series
CASE Switch Start
no selecte seriesmessage
No Molecular Series Selected
identify_mol_seriesswitch stop(mol activity)
CASE Switch End
it just propagate theactive/inactive branch
Table Row to Variable
Molecular Series Configuration
Molecular Series Tuning
this simply propagatesactives/inactives branches
Table Row to Variable
Display Individual Activities & References
Display Aggregated Activitiy
render the structure ofthe top 2K mols
Molecule Structure Renderer
Molecule Activity Aggregation
Use molecule chembl_id(potentially concatenated for salts)as molID/row/IDand select activity meadian as activity
use chembl_id as molID/rowID
it retrieves activity data fromactivity_id list
retrieve activity data from activity ids
missing_target_search_keywords
Rule Engine Variable
ChEMBL Molecular Series Details
ChEMBL Activity Type Selection
missing_target_searchkeyword switch start
CASE Switch Start
No Target Selected
mol_act_cols_regex
String Manipulation (Variable)
inject vars
Inject Variables (Data)
ChEMBL Target Search Configuration
Workflow intro
ChEMBL Activity Type Retrieval
Salt Stripper
missing_target_searchkeyword switch end
CASE Switch End
Empty Table Switch
ChEMBL Target Search
Molecules vs Series Selection
Molecular Series Identification
Cols & Vars handling
No Activity Type Selected
mol_act_cols_regex
String Manipulation (Variable)
ChEMBL Activity Retrieval
sort by mol_act desc
Sorter
Text View
activate bottom if no activity type selected
Empty Table Switch

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: 2022-10-17
On NodePit since: 2026-06-23
Last update: 2026-08-02
Created with KNIME version: v5.8.1
Tags: vanilla workflow

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