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mTOR

TeachOpenCADD Workflow 1: Data acquisition from ChEMBL

Information on compound structure, bioactivity, and associated targets are organized in databases such as ChEMBL, PubChem, or DrugBank.
This workflow shows how to obtain and preprocess data for a query target (default target: EGFR) from the ChEMBL web services.

Scorer
Add pIC50
Math Formula
MCS
Metanode
Rule Engine
Only SMILES present
Row Filter (deprecated)
Excel Writer
Rule Engine
String Manipulation
Row Sampler
MultiLayerPerceptron Predictor
Row Splitter
Excel Writer
Scorer
Concatenate
Scorer
Train modelon training set
Random Forest Learner
ROC Curve (legacy)
RProp MLP Learner
ROC Curve (legacy)
ROC Curve (legacy)
SVM Learner
SVM Predictor
Table View
Molecule Type Cast
Split fingerprint to one bit per column
Expand Bit Vector
Train modelon training set
Random Forest Learner
GroupBy
RDKit Find Murcko Scaffolds
Reference Row Splitter
Test modelon test set
Random Forest Predictor
Table Partitioner
Reference Row Splitter
Column Filter
Add boolean activity column
Math Formula
Reference Row Splitter
Table View (JavaScript) (legacy)
Column Filter
SVM Predictor
Table Partitioner
SVM Learner
Get activities count
Parameter Optimization Loop End
Parameter Optimization Loop Start
ROC Curve (legacy)
Ca. 10s per 1000 mols
Get activities
Scorer
ROC Curve (legacy)
Scorer
ROC Curve (legacy)
Scorer
Parameter Optimization Loop Start
Convert all molar units to nM
Java Snippet
Only IC50
Row Filter (deprecated)
RDKit From Molecule
Only nM
Row Filter (deprecated)
No duplicates
GroupBy
String to Number
Only binding assay data
Row Filter (deprecated)
Input target ChEMBL ID
Only exactmeasurements
Row Filter (deprecated)
Excel Writer
Only molar units
Row Filter (deprecated)
Column Renamer
Column Filter
RProp MLP Learner
Column Resorter
Excel Writer
Parameter Optimization Loop End
Column Resorter
Generate fingerprint(default MACCS)
RDKit Fingerprint
Parameter Optimization Loop End
MultiLayerPerceptron Predictor
Parameter Optimization Loop Start
Random Forest Predictor

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: dominique
Created at: 2019-07-15
On NodePit since: 2026-05-21
Last update: 2026-05-21
Created with KNIME version: v5.11.0
Tags: ChEMBLWeb service queryData filtering & formatting

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