MORTAR: a rich client application for in silico molecule fragmentation

Felix Bänsch; Jonas Schaub; Betül Sevindik; Samuel Behr; Julian Zander; Christoph Steinbeck; Achim Zielesny

doi:10.1186/s13321-022-00674-9

MORTAR: a rich client application for in silico molecule fragmentation

J Cheminform. 2023 Jan 2;15(1):1. doi: 10.1186/s13321-022-00674-9.

Authors

Felix Bänsch¹, Jonas Schaub², Betül Sevindik¹, Samuel Behr¹, Julian Zander¹, Christoph Steinbeck², Achim Zielesny³

Affiliations

¹ Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany.
² Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.
³ Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany. achim.zielesny@w-hs.de.

Abstract

Developing and implementing computational algorithms for the extraction of specific substructures from molecular graphs (in silico molecule fragmentation) is an iterative process. It involves repeated sequences of implementing a rule set, applying it to relevant structural data, checking the results, and adjusting the rules. This requires a computational workflow with data import, fragmentation algorithm integration, and result visualisation. The described workflow is normally unavailable for a new algorithm and must be set up individually. This work presents an open Java rich client Graphical User Interface (GUI) application to support the development of new in silico molecule fragmentation algorithms and make them readily available upon release. The MORTAR (MOlecule fRagmenTAtion fRamework) application visualises fragmentation results of a set of molecules in various ways and provides basic analysis features. Fragmentation algorithms can be integrated and developed within MORTAR by using a specific wrapper class. In addition, fragmentation pipelines with any combination of the available fragmentation methods can be executed. Upon release, three fragmentation algorithms are already integrated: ErtlFunctionalGroupsFinder, Sugar Removal Utility, and Scaffold Generator. These algorithms, as well as all cheminformatics functionalities in MORTAR, are implemented based on the Chemistry Development Kit (CDK).

Keywords: CDK; Chemistry Development Kit; Functional groups; GUI; Glycosidic moieties; Graphical user interface; In silico fragmentation; Molecule fragmentation; Rich client; Scaffolds.