PubChem Search

Search data by structure, substructure and similarity to PubChem. The node uses the PubChem Power User Gateway (PUG) service. https://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html In the PUG, the node is connecting to the server via HTTPS and FTP protocols during execution process. Therefore, your network has to use both of HTTPS and FTP protocols.

Options

Query structure column: The query structure column.
Search type: Sets different search options according to a predefined search type.
Identity search options: Additional options are provided to return all structures identical to this structure using different notions of chemical structure identity.
Similarity threshold: The degree of similarity is dictated by the Threshold parameter.
Stereochemistry: Sets matching stereochemistry.
Match isotopes: Indicates that the isotopic information within the query is to be used.
Match charges: Indicts that the formal charge information within the query is to be used.
Match tautomers: Indicates that tautomers of the query are allowed to match.
Ringsystems not embedded: Indicates that the results should exactly match the ring systems as they are provided in the query.
Single/double bonds match aromatic bonds: Indicates that singe or double bonds in the query may match aromatic bonds.
Chain bonds match ring bonds: Indicated that chain bonds in the query may match both ring and chain bonds.
Strip hydrogen: Indicates that explicit hydrogen in the query is to be removed prior to searching.
Time Limit: Sets time limit (in CPU seconds).
Result Limit: Sets hit limit count.
Select fields: Selects PubChem System Utilized SD Fields.

Input Ports

: Input table that contains query structure in Structure(Mrv, Sdf, Smiles, etc.) format.

Output Ports

: Output table that contains search result structure in Marvin format.

Popular Successors

Views

This node has no views

Workflows

No workflows found

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

Installation

To use this node in KNIME, install the extension ChemAxon/Infocom JChem Extensions Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.9

A zipped version of the software site can be downloaded here.

Plugin provider: Infocom Corporation

Plugin version: 4.7.0.v250304

On NodePit since: 2025-12-17

Last update: 2026-01-11

KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!