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Bioinformatics & Cheminformatics

Molpher (Software tool for exploration of the chemical space)

Molpher aims to be a scalable and interactive software tool to aid exploration of chemical space, the vast universe containing all possible compounds. Many areas of chemical biology, such as drug discovery, rely heavily on chemical libraries offering compounds usable in the industrial processes. Given a set of molecules with desired characteristics, Molpher explores their common neighbourhood based on structural similarity, as it represents promising part of the chemical space to find new additions into those libraries. In order to decrease the chance of missing interesting parts of the space, Molpher offers the human researcher to observe and interactively alter the exploration process. Generated subspace is expected to be further tested for synthesizability and biological activity by other software tools.

Among main features, Molpher offers optimized parallel exploration algorithm, compound logging, dimension-reduced visualization of chemical space and interactive widget-based GUI. Codebase is extensible in terms of additional morphing operators, chemical fingerprints, similarity measures and visualization strategies to allow further experiments.

David Hoksza, Petr Škoda
ViFrame (Chemical space visualization framework)


ViFrame is a modular framework targeted at chemical space visualization task. It offers a simple implementation of every single part of the visualization pipeline consisting of steps such as reading and merging molecules from multiple data sources, applying transformations and finally visualization of the data set in 2D space. The framework also incorporates an application that provides the user with graphical
interface for modules manipulation and presentation of the visualization results. For simple utilization of the application without the necessity of implementation of one’s own module, several visualization methods are implemented and delivered with the project.
David Hoksza, Petr Škoda