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Home Chemspace KNIME Nodes

Chemspace KNIME Nodes

KNIME Analytics Platform is a powerful open source tool for data mining. We have created the Chemspace nodes for KNIME that allow to search directly in Chemspace database (100 million compounds) without using your browser.

We provide two nodes for searching in the Chemspace database: Structure Search and simple ID Search.

You can embed Chemspace nodes into your custom in-house workflow, get the information on marketed compounds and post-process the search results in any desired way.

To use the nodes, you will need the Chemspace API Key that we will send via email. Contact us at info@chem-space.com to request the Key.

You can get up to 200 results per each query performing up to 40 requests per minute.

What should be the input?

Structure Search node accepts String cells with SMILES. Please see the Example Workflow for more details.

What is the output?

For each query where results are found, the nodes generate output with SMILES, Chemspace IDs, and URLs. If Similarity Search is selected, Tanimoto Similarity column is added.

How to use the nodes?

Please see our Example Workflow to explore the features of the Chemspace nodes.

Chemspace Search node allows you to search by chemical structure. You can draw the structure or write down the SMILES, load SMILES from a file, or convert structure file into SMILES. Then, convert your SMILES cell into String cell. You can use String Manipulation, String Replacer or Column rename node for converting the cell.

Chemspace Search allows you to set: the column with your query molecules, search type, similarity threshold for Similarity Search, and number of hits per query.

There are three search options available: Exact Match, Substructure Search, and Similarity Search (ECFP4 fingerprints, 1024 bit).

Substructure and Similarity Search options are available for Screening Compounds and Building Blocks separately.


Chemspace ID Search node allows to search in Chemspace database by the identifier. The node works with Chemspace IDs or Chemspace vendor’s ID.

The node allows you to choose the column with identifiers to be searched for. Data in the column should be of String type.

How to install Chemspace Search nodes?

  1. Launch KNIME.
  2. Open Help menu and click Install New Software.

  3. Type https://chem-space.com/knime/ into the Work with field.

  4. Tick the Chemspace KNIME nodes checkbox.

  5. Click next and follow the further instructions.
  6. For changes to take effect, you will need to restart KNIME. When the installation is complete, the application will propose you to restart it.
  7. You can find Chemspace nodes in your Node Repository after the restart