KNIME Hub Authenticator
Authenticates against a KNIME Hub. Learn more
Collection
KNIME for Chemistry
This curated set of workflow snippets is specifically designed to provide cheminformatics users with essential building blocks for developing their own customized workflows within the KNIME Analytics Platform. Rather than offering complete workflows for entire use cases, this collection focuses on individual components that you can combine. Explore the collection, experiment with the snippets, and discover how KNIME can enhance your cheminformatics projects.
KNIME in Life Science
Explore how KNIME empowers cheminformatics with flexible tools and workflows tailored for molecular data processing, analysis, and visualization.
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Data Access
This section provides tools for importing and managing chemical data from multiple sources. It includes workflows for fetching molecular structures from PDB with 3D visualization, retrieving SMILES strings from PubChem CIDs, and handling data through JSON, XML, or GraphQL queries. Additionally, it supports reading data from Excel files, SDF files, and mixed folders, ensuring smooth integration of diverse inputs into your workflows.
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Sketching a Molecule
Generates chemical structures by allowing users to draw and modify molecules based on input SMILES.
Life SciencesCollectionsChemistry with KNIME01 InputSketching a Molecule
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SDF Reading
Example workflow for loading SDF files containing molecules.
Life SciencesCollectionsChemistry with KNIME01 InputSDF Reading
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Fetch Data from SQLite Database
Retrieves data from an SQLite database, showcasing in-database filtering before loading the data to save computational resources.
Life SciencesCollectionsChemistry with KNIME01 InputFetch Data from SQLite Database
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GET Request (JSON Response)
Retrieves genetic information from the MyGene.info REST service and parses the JSON response into a readable table.
Life SciencesCollectionsChemistry with KNIME01 InputGET Request (JSON Response)
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GET Request (XML response)
Extracts data from XML response of a GET request using XPath.
Life SciencesCollectionsChemistry with KNIME01 InputGET Request (XML response)
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Fetch SMILES for Pubchem CIDs (POST Request)
Retrieves SMILES for PubChem IDs using a POST request.
Life SciencesCollectionsChemistry with KNIME01 InputFetch SMILES for Pubchem CIDs (POST Request)
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Find and View PDB Data
Queries the PDB using Vernalis nodes and visualizes the results in 3D using the 3D Molecule Viewer.
Life SciencesCollectionsChemistry with KNIME01 InputFind and View PDB Data
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Query GraphQL API
Retrieves information by using the GraphQL API of the Opentargets Platform.
Life SciencesCollectionsChemistry with KNIME01 InputQuery GraphQL API
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Processing
Here, you will find tools for converting strings to SMILES, sanitizing query SMARTS, standardizing molecular structures, and generating molecular coordinates to align molecules. These building blocks help you efficiently process and prepare your chemical data.
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Workflow
Convert a string to SMILES
Using molecules within KNIME can necessitate converting string type to SMILES type for molecular interpretation.
Life SciencesCollectionsChemistry with KNIME02 ManipulationConvert a string to SMILES
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Standardizing Molecular Structures
Standardizes chemical structures in SMILES format.
Life SciencesCollectionsChemistry with KNIME02 ManipulationStandardizing Molecular Structures
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Sanitize SMARTS and Generate Coordinates for a Molecule
Generates sanitized SMARTS for molecule alignment.
Life SciencesCollectionsChemistry with KNIME02 ManipulationSanitize SMARTS and Generate Coordinates for a Molecule
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Analysis
This category focuses on data exploration. This includes snippets for calculating molecular properties and descriptors, counting specific elements in molecules, or generating and comparing chemical fingerprints.
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Descriptor Calculation
Calculate molecular descriptors/properties using free extensions.
Life SciencesCollectionsChemistry with KNIME03 AnalysisDescriptor Calculation
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Fingerprint Generation and Comparison
Generates chemical fingerprints from input molecules using different methods, and compares the results.
Life SciencesCollectionsChemistry with KNIME03 AnalysisFingerprint Generation and Comparison
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Count an Element in a Molecule
Counts the number of atoms in a molecule for a chosen element using the RDKit Substructure Counter.
Life SciencesCollectionsChemistry with KNIME03 AnalysisCount an Element in a Molecule
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Visualization
For reporting and exporting results, this section includes workflows for generating reports, such as creating reports from composite views, be it overviews or page-by-page reporting with loops. Additionally, you’ll find workflows for writing images to Excel, formatting Excel outputs, and integrating execution dates into filenames.
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Create Hyperlinks in Table View
Generates hyperlinks in Table Views, in this example for PubMed IDs.
Life SciencesCollectionsChemistry with KNIME04 VisualizationCreate Hyperlinks in Table View
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Add Colors to Table Cells
Append colours to individual cells depending on the value.
Life SciencesCollectionsChemistry with KNIME04 VisualizationAdd Colors to Table Cells
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Assigning Custom Colors to Columns
Assigns custom colors to columns in charts based on specified data attributes.
Life SciencesCollectionsChemistry with KNIME04 VisualizationAssigning Custom Colors to Columns
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Output
This category includes workflow snippets for exporting and reporting your cheminformatics results. This section offers workflows for generating reports, such as creating reports from composite views, be it overviews or page-by-page reporting with loops. Additionally, you’ll find workflows for writing images to Excel, formatting Excel outputs, and integrating execution dates into filenames.
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Report generation from a composite view
Generates a report combining molecules and data from bioactivity prediction results.
Life SciencesCollectionsChemistry with KNIME05 OutputReport generation from a composite view
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Write molecule images to Excel
Integrates molecule images in Excel output.
Life SciencesCollectionsChemistry with KNIME05 OutputWrite molecule images to Excel
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Excel Formatting
Formats Excel files by applying conditional formatting, changing the font, and adjusting column width based on a control table te…
Life SciencesCollectionsChemistry with KNIME05 OutputExcel Formatting
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Integrate Execution Date in File Name
Automatically adds execution date to file name to prevent overwriting the previous day's file.
Life SciencesCollectionsChemistry with KNIME05 OutputIntegrate Execution Date in File Name
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Business Hub Integration
Integrate your workflows into the KNIME Business Hub to scale and automate cheminformatics processes. Below are listed nodes for connecting your workflows with the KNIME Business Hub enable deployment management, file transfers, and secure credential handling. Use these nodes to automate processes, streamline collaboration, and scale your cheminformatics workflows.
File Upload and Download in Business Hub
Examples demonstrating how to upload and download files within the KNIME Business Hub using specific workflows and components.
Cheminformatics Extensions
Explore a variety of free and commercial extensions for cheminformatics in KNIME.
Free Trusted Extensions
Explore a collection of free trusted extensions for KNIME
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Extension
RDKit
This feature contains several nodes that provide some of RDKit functionality.
Novartis
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CDK
This feature contains several nodes that are suitable for processing chemical data.
University Konstanz and EBI
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Extension
Vernalis KNIME Nodes
This feature contains Vernalis KNIME nodes extensions
Vernalis Research Ltd, Cambridge, UK
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Commercial Extensions
This subsection contains commercial extensions for KNIME.
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Extension
Chemaxon
The JChem Extensions offers a set of KNIME nodes with chemical data.
Infocom Corporation
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Extension
Schrödinger
This feature contains Schrodinger data types, Schrödinger nodes and Canvas 2D renderers.
Schrödinger
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Extension
MOE
Nodes, renderers and data types for molecular modeling based on the Molecular Operating Environment MOE.
Chemical Computing Group ULC.
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Additional Resources
This section includes material about KNIME Python integration, teaching resources like TeachOpenCADD, and articles about screening and filtering. You’ll find tutorials and case studies, as well as a collection of scientific publications demonstrating how KNIME has been used in cheminformatics research and drug discovery.
Useful Cheminformatics Components
Ready-to-use components designed to simplify and enhance common cheminformatics operations within your workflows
KNIME Python integration
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Collection
Getting started with KNIME Python integration
Provides an overview of KNIME Python integration and how Python scripts can be used within KNIME workflows.
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Teaching with KNIME: The TeachOpenCADD project
Resources for learners and educators using KNIME in cheminformatics, created by the Volkamer group.