GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics

M Sicho; X Liu; D Svozil; G J P van Westen

doi:10.1186/s13321-021-00550-y

GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics

J Cheminform. 2021 Sep 25;13(1):73. doi: 10.1186/s13321-021-00550-y.

Authors

M Sicho^#¹, X Liu^#², D Svozil^{1

3}, G J P van Westen⁴

Affiliations

¹ CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague, Czech Republic.
² Computational Drug Discovery, Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands.
³ CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
⁴ Computational Drug Discovery, Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands. gerard@lacdr.leidenuniv.nl.

^# Contributed equally.

Abstract

Many contemporary cheminformatics methods, including computer-aided de novo drug design, hold promise to significantly accelerate and reduce the cost of drug discovery. Thanks to this attractive outlook, the field has thrived and in the past few years has seen an especially significant growth, mainly due to the emergence of novel methods based on deep neural networks. This growth is also apparent in the development of novel de novo drug design methods with many new generative algorithms now available. However, widespread adoption of new generative techniques in the fields like medicinal chemistry or chemical biology is still lagging behind the most recent developments. Upon taking a closer look, this fact is not surprising since in order to successfully integrate the most recent de novo drug design methods in existing processes and pipelines, a close collaboration between diverse groups of experimental and theoretical scientists needs to be established. Therefore, to accelerate the adoption of both modern and traditional de novo molecular generators, we developed Generator User Interface (GenUI), a software platform that makes it possible to integrate molecular generators within a feature-rich graphical user interface that is easy to use by experts of diverse backgrounds. GenUI is implemented as a web service and its interfaces offer access to cheminformatics tools for data preprocessing, model building, molecule generation, and interactive chemical space visualization. Moreover, the platform is easy to extend with customizable frontend React.js components and backend Python extensions. GenUI is open source and a recently developed de novo molecular generator, DrugEx, was integrated as a proof of principle. In this work, we present the architecture and implementation details of GenUI and discuss how it can facilitate collaboration in the disparate communities interested in de novo molecular generation and computer-aided drug discovery.

Keywords: De novo drug design; Deep learning; Graphical user interface; Molecule generation; Web application.

Abstract

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