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MORTAR: a rich client application for in silico molecule fragmentation

  • 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).

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Author:Felix Bänsch, Jonas Schaub, Betül Sevindik, Samuel Behr, Julian Zander, Christoph Steinbeck, Achim Zielesny
Parent Title (English):Journal of Cheminformatics
Document Type:Article
Date of Publication (online):2023/01/02
Date of first Publication:2023/01/02
Publishing Institution:Westfälische Hochschule Gelsenkirchen Bocholt Recklinghausen
Release Date:2023/06/22
Tag:Chemistry Development Kit, CDK, Molecule fragmentation, In silico fragmentation, Scaffolds, Functional groups, Glycosidic moieties, Rich client, Graphical user interface, GUI
Issue:15, 1
Departments / faculties:Institute / Institut für biologische und chemische Informatik
Licence (German):License LogoEs gilt das Urheberrechtsgesetz

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