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 [link].
Nodes
- Column Filter79 ×
- String Manipulation (Variable)70 ×
- CASE Switch End68 ×
- String Manipulation67 ×
- CASE Switch Start60 ×
- Column Renamer47 ×
- Joiner40 ×
- Table Row to Variable40 ×
- String Configuration39 ×
- RowID38 ×
- Single Selection Configuration38 ×
- Rule Engine Variable36 ×
- Merge Variables31 ×
- Sorter25 ×
- Column Resorter24 ×
- GroupBy22 ×
- Integer Configuration21 ×
- Text View21 ×
- Reference Row Filter19 ×
- Row Filter18 ×
- Column Rename16 ×
- Cross Joiner15 ×
- Renderer to Image15 ×
- Table View (JavaScript)15 ×
- Column Splitter13 ×
- Transpose13 ×
- Cell Splitter12 ×
- Column Selection Configuration12 ×
- Concatenate12 ×
- Empty Table Creator12 ×
- Variable to Table Row12 ×
- Extract Column Header11 ×
- Inject Variables (Data)11 ×
- Column Rename (Regex)10 ×
- Column Splitter10 ×
- Math Formula10 ×
- Ungroup10 ×
- DB Query Reader (Labs)9 ×
- Domain Calculator9 ×
- Interactive Value Filter Widget9 ×
- Color Manager8 ×
- Constant Value Column Appender8 ×
- Extract Table Dimension8 ×
- Interactive Range Slider Filter Widget8 ×
- Empty Table Switch7 ×
- Expand Byte Vector7 ×
- File Download Widget7 ×
- Table Creator7 ×
- Text Output Widget7 ×
- Boolean Configuration6 ×
- CSV Writer6 ×
- Constant Value Column6 ×
- Counter Generation6 ×
- Create Temp Folder6 ×
- Duplicate Row Filter6 ×
- Hierarchical Cluster Assigner (JavaScript)6 ×
- Java Snippet (simple)6 ×
- Number To String6 ×
- Numeric Distances6 ×
- Path to String (Variable)6 ×
- PostgreSQL Connector (Labs)6 ×
- Reference Column Filter6 ×
- Row Splitter6 ×
- Row Splitter6 ×
- SQLite Connector (Labs)6 ×
- String to Date&Time6 ×
- DB Looper5 ×
- DB Table Selector5 ×
- Expand Bit Vector5 ×
- Loop End5 ×
- RDKit Count-Based Fingerprint5 ×
- RDKit Fingerprint5 ×
- Rule Engine5 ×
- Scatter Plot (JavaScript)5 ×
- Column Auto Type Cast4 ×
- Column Combiner4 ×
- Insert Column Header4 ×
- Hierarchical Clustering (DistMatrix)4 ×
- RDKit To Molecule4 ×
- Reference Column Resorter4 ×
- Refresh Button Widget4 ×
- String To Number4 ×
- Boolean Widget3 ×
- Create Collection Column3 ×
- Group Loop Start3 ×
- PCA Apply3 ×
- PCA Compute3 ×
- RDKit Find Murcko Scaffolds3 ×
- RDKit To InChI3 ×
- Reference Row Splitter3 ×
- Row Filter3 ×
- Single Selection Widget3 ×
- Tile View (JavaScript)3 ×
- t-SNE (L. Jonsson)3 ×
- Bit Vector Distances2 ×
- Byte Vector Distances2 ×
- Chunk Loop Start2 ×
- Column Filter Configuration2 ×
- Column Filter Widget2 ×
- Distance Matrix Calculate2 ×
- Distance Matrix Pair Extractor2 ×
- Double Widget2 ×
- Hierarchical Cluster Assigner2 ×
- Integer Widget2 ×
- Math Formula (Variable)2 ×
- Missing Value2 ×
- Molecule Type Cast2 ×
- PCA2 ×
- Parameter Optimization Loop End2 ×
- Parameter Optimization Loop Start2 ×
- RDKit From Molecule2 ×
- RDKit Substructure Filter2 ×
- Silhouette Coefficient2 ×
- Sunburst Chart (JavaScript) (legacy)2 ×
- Variable Expression2 ×
- Autocomplete Text Widget1 ×
- Box Plot (JavaScript) (legacy)1 ×
- CSS Editor1 ×
- Color Appender1 ×
- Column List Loop Start1 ×
- Credentials Configuration1 ×
- Double Configuration1 ×
- Excel Writer1 ×
- Expression1 ×
- Extract Variables (Data)1 ×
- Histogram1 ×
- Image To Table1 ×
- KNIME Hub Authenticator1 ×
- Local File Browser Configuration1 ×
- Loop End (Column Append)1 ×
- Round Double1 ×
- RDKit Descriptor Calculation1 ×
- RDKit Salt Stripper1 ×
- Secrets Retriever1 ×
- Table Validator (Reference)1 ×
Extensions
- FeatureKNIME Base Chemistry Types & Nodes
- FeatureKNIME Base nodes
- FeatureKNIME Data Generation
- FeatureKNIME Database
- FeatureKNIME Distance Matrix
- Show all 19 modules
Links
- No links available