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Chemspace Search

Chemspace Search Node extension for KNIME Workbench version 1.7.4 by Chemspace

This node performs chemical or ID search in Chemspace database through Chemspace API (over 1.3B compounds). Either SMILES or ID; Chemspace ID, vendor ID, REAL Space/Database ID could be used as query.

Available search options for structure search:

ID search:: returns, if available, structures from Chemspace database that correspond to the identifiers;

Exact search: returns exact match per query (if available);

Substructure search: returns up to 2000 hits per query molecule fragment;

Similarity Search: returns up to 2000 top hits by Tanimoto similarity (ECFP4, 1024)

Also, search in separate sections of Chemspace database is available:

– CSSB – in-stock Building Blocks

– CSSS – in-stock Screening Compounds

– CSMB – make-on-demand Building Blocks

– CSMS – make-on-demand Screening Compounds

– CSCS – custom synthesis

Please find more information about our database sections here: https://chem-space.com/search

Chemspace API Key is needed to use this node. To obtain the Key, please contact us at info@chem-space.com.

Please note that with your Key you can perform a limited number of requests per minute (40).

Options

Chemspace API Key
A text field that accepts Chemspace API Key. The key is obtained via email.
Search type radio buttons
ID Search, Exact Search, Substructure Search, Similarity Search.
Search in categories checkboxes
Select which sections of Chemspace database you wish to use (find out more about them at https://chem-space.com/search).
Maximum hits per query
An Integer field that sets maximum number of results per query.The value is limited to 2000.
Show PhysChem parameters checkbox
A checkbox that defines if the pre-calculated PhysChem parameters (MW, Heavy Atoms, ClogP, Rotatable Bonds, H-bond Acceptors, H-bond Donors, Rings, Fsp3, TPSA) will be displayed for hits (unchecked by default).

Input parameters for port 'Input query'

Query ID
Identifiers to be searched if “search by ID” is selected as search type.
Query SMILES
SMILES to be searched if “exact search”, “substructure search” or “similarity search” is selected as search type.

Output parameters for port 'Found in Chemspace'

Chemspace SMILES
Chemspace SMILES for found compound.
Chemspace ID
Chemspace identifier for the hit from REAL database.
Chemspace URL
Link to the search result on Chemspace website
Query ID / Query SMILES
Query that have been used in the search.
Search Type
Selected search type.
PhysChem parameters
MW, Heavy Atoms, ClogP, Rotatable Bonds, H-bond Acceptors, H-bond Donors, Rings, Fsp3, TPSA if the corresponding checkbox was selected.

Output parameters for port 'No hits'

Query ID / Query SMILES
Query that have been used in the search.
Search Type
Chemical search type.
Search Result Message
Search result message.

Input Ports

Icon
Input query – table that contains column with SMILES (string or smiles format) or column with identifiers (string or numeric format).

Output Ports

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Found in Chemspace: Returns the input table with 4 columns added: Chemspace SMILES, Chemspace ID, Chemspace URL, and Search Type. Multiple search results (for Substructure or Similarity Search) are presented in additional rows. Column with queries will be renamed to “Query SMILES” or “Query ID” accordingly to the search type.
Icon
No hits: Returns the input table with queries for which no hits were found with 2 columns added: Search Type, and Search Result Message.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install ChemSpace KNIME Nodes from the following update site:

KNIME 4.3

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