MONA – Interactive manipulation of molecule collections

Working with small‐molecule datasets is a routine task forcheminformaticians and chemists. The analysis and comparison of vendorcatalogues and the compilation of promising candidates as starting pointsfor screening campaigns are but a few very common applications. Theworkflows applied for this purpose usually consist of multiple basiccheminformatics tasks such as checking for duplicates or filtering byphysico‐chemical properties. Pipelining tools allow to create andchange such workflows without much effort, but usually do not supportinterventions once the pipeline has been started. In many contexts, however,the best suited workflow is not known in advance, thus making it necessaryto take the results of the previous steps into consideration beforeproceeding.To support intuition‐driven processing of compound collections, wedeveloped MONA, an interactive tool that has been designed to prepare andvisualize large small‐molecule datasets. Using an SQL database commoncheminformatics tasks such as analysis and filtering can be performedinteractively with various methods for visual support. Great care was takenin creating a simple, intuitive user interface which can be instantly usedwithout any setup steps. MONA combines the interactivity of moleculedatabase systems with the simplicity of pipelining tools, thus enabling thecase‐to‐case application of chemistry expert knowledge. Thecurrent version is available free of charge for academic use and can bedownloaded at http://www.zbh.uni-hamburg.de/mona.