KNIME Workflow to Assess PAINS Filters in SMARTS Format. Comparison of RDKit and Indigo Cheminformatics Libraries

Simon Saubern; Rajarshi Guha; Jonathan B. Baell

doi:10.1002/minf.201100076

August 4, 2011Molecular Informatics

KNIME Workflow to Assess PAINS Filters in SMARTS Format. Comparison of RDKit and Indigo Cheminformatics Libraries

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Key Points

Develop and evaluate a KNIME workflow to assess pan-assay interference compounds (PAINS) filters encoded in SMARTS format across different cheminformatics software libraries.
Constructed automated analytical workflows in the KNIME platform to parse and evaluate PAINS substructure definitions.
Benchmarked chemical pattern matching using both the RDKit and Indigo open-source cheminformatics toolkits.
Demonstrated operational variations between RDKit and Indigo when interpreting complex SMARTS queries for molecular filtering.
Established a standardized workflow to help computational chemists identify and resolve discrepancies in compound screening filters.

Implication

Computational study compares SMARTS-based PAINS filter performance across chemical libraries in KNIME, highlighting implementation differences between RDKit and Indigo.

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Cite This Study

Saubern et al. (2011) studied this question.

synapsesocial.com/papers/6a15ddd7a215942ca9e3cee4 https://doi.org/10.1002/minf.201100076

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KNIME Workflow to Assess PAINS Filters in SMARTS Format. Comparison of RDKit and Indigo Cheminformatics Libraries

Key Points

Implication

Abstract

Discussion

Cite This Study

KNIME Workflow to Assess PAINS Filters in SMARTS Format. Comparison of RDKit and Indigo Cheminformatics Libraries

Key Points

Implication

Abstract

Discussion

Cite This Study

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Keep reading

More from Molecular Informatics