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Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

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chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery.

Man-Ling Lee¹, Ignacio Aliagas², Jianwen A Feng³

¹Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA. lee.man-ling@gene.com.

Journal of Cheminformatics

|November 1, 2017

Summary

The chemalot and chemalot_knime open source packages offer powerful cheminformatics tools. These packages streamline workflow creation and analysis, integrating command-line programs into KNIME for enhanced data investigation and model building.

Keywords:

Command line program Conformation analysis Dynamic KNIME node generation Property calculation QSPR model SAR Strain energy analysis Substructure identification

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Area of Science:

Cheminformatics
Computational Chemistry
Bioinformatics

Background:

Cheminformatics analysis relies on diverse workflows.
Open-source packages chemalot and chemalot_knime are introduced.
Chemalot provides command-line functionalities; chemalot_knime integrates these into KNIME nodes.

Purpose of the Study:

To present the chemalot and chemalot_knime packages for cheminformatics.
To demonstrate the integration of command-line tools within KNIME workflows.
To leverage Linux cluster compute power for cheminformatics tasks.

Main Methods:

Utilizing chemalot command-line programs for data manipulation.
Wrapping command-line tools into KNIME nodes using chemalot_knime.
Developing and executing workflows in KNIME for cheminformatics analysis.

Main Results:

Demonstrated workflows for creating project-specific data files.
Successfully built quantitative structure-property-relationship models via KNIME nodes.
Analyzed strain energy in small molecule ligand conformations from the Protein Data Bank.

Conclusions:

Chemalot and chemalot_knime are lightweight, powerful cheminformatics tools.
These packages facilitate integration with other cheminformatics tools.
Chemalot_knime simplifies user-defined workflow generation and maintenance within KNIME.