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

0555488 - ÚMG 2022 RIV GB eng J - Journal Article
Šícho, M. - Liu, X. - Svozil, Daniel - van Westen, G.J.P.
GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics.
Journal of Cheminformatics. Roč. 13, č. 1 (2021), č. článku 73. ISSN 1758-2946. E-ISSN 1758-2946
R&D Projects: GA MŠMT(CZ) LM2018130
Research Infrastructure: CZ-OPENSCREEN III - 90130
Institutional support: RVO:68378050
Keywords : Graphical user interface * De novo drug design * Molecule generation * Deep learning * Web application
OECD category: Biochemistry and molecular biology
Impact factor: 8.489, year: 2021
Method of publishing: Open access
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00550-y

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.
Permanent Link: http://hdl.handle.net/11104/0329996