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Open Access Software

Template-based combinatorial enumeration of virtual compound libraries for lipids

Manish Sud1, Eoin Fahy1 and Shankar Subramaniam12

Author Affiliations

1 San Diego Supercomputer Center, University of California San Diego, 9500, Gilman Drive, La Jolla, CA 92032, USA

2 Departments of Bioengineering, Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

Journal of Cheminformatics 2012, 4:23  doi:10.1186/1758-2946-4-23

Published: 25 September 2012

Abstract

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license.

Graphical abstract