MORTAR: a rich client application for in silico molecule fragmentation.

Area of Science:

• Computational chemistry
• Cheminformatics
• Software development

Background:

• Developing in silico molecule fragmentation algorithms is an iterative process requiring a specialized computational workflow.
• Existing workflows are often unavailable for new algorithms, necessitating individual setup.
• This hinders the efficient development and accessibility of novel fragmentation tools.

Purpose of the Study:

• To present MORTAR, an open Java GUI application designed to facilitate the development and integration of new in silico molecule fragmentation algorithms.
• To provide a standardized computational workflow for algorithm implementation, testing, and visualization.
• To make developed fragmentation algorithms readily available upon release.

Main Methods:

• Developed an open Java rich client Graphical User Interface (GUI) application named MORTAR (MOlecule fRagmenTAtion fRamework).
• Implemented a wrapper class for integrating and developing new fragmentation algorithms within MORTAR.
• Utilized the Chemistry Development Kit (CDK) for all cheminformatics functionalities and integrated three initial algorithms: ErtlFunctionalGroupsFinder, Sugar Removal Utility, and Scaffold Generator.

Main Results:

• MORTAR provides a unified environment for in silico molecule fragmentation algorithm development.
• The application visualizes fragmentation results and offers basic analysis features.
• Fragmentation pipelines can be created by combining available methods within MORTAR.

Conclusions:

• MORTAR simplifies and accelerates the development cycle of in silico molecule fragmentation algorithms.
• The application enhances the accessibility and usability of novel fragmentation tools.
• MORTAR, built on the Chemistry Development Kit, offers a robust framework for cheminformatics research.