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Open Access Highly Accessed Open Badges Methodology article

Natural product-likeness score revisited: an open-source, open-data implementation

Kalai Vanii1*, Pablo Moreno1, Andreas Truszkowski2, Peter Ertl3 and Christoph Steinbeck1*

Author Affiliations

1 Chemoinformatics and Metabolism, European Bioinformatics Institute (EBI), Cambridge, UK

2 Institute for Bioinformatics and Cheminformatics, University of Applied Sciences of Gelsenkirchen, Germany

3 Novartis Institutes for BioMedical Research, , Switzerland

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BMC Bioinformatics 2012, 13:106  doi:10.1186/1471-2105-13-106

Published: 20 May 2012



Natural product-likeness of a molecule, i.e. similarity of this molecule to the structure space covered by natural products, is a useful criterion in screening compound libraries and in designing new lead compounds. A closed source implementation of a natural product-likeness score, that finds its application in virtual screening, library design and compound selection, has been previously reported by one of us. In this note, we report an open-source and open-data re-implementation of this scoring system, illustrate its efficiency in ranking small molecules for natural product likeness and discuss its potential applications.


The Natural-Product-Likeness scoring system is implemented as Taverna 2.2 workflows, and is available under Creative Commons Attribution-Share Alike 3.0 Unported License at webcite. It is also available for download as executable standalone java package from webciteunder Academic Free License.


Our open-source, open-data Natural-Product-Likeness scoring system can be used as a filter for metabolites in Computer Assisted Structure Elucidation or to select natural-product-like molecules from molecular libraries for the use as leads in drug discovery.