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

G J P Van Westen,D Svozil,M Sicho,X Liu

doi:10.1186/s13321-021-00550-y

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.

Highlights

Due to significant technological advances in the past decades, the body of knowledge on the effects and roles of small molecules in living organisms has grown tremendously [1, 2]
De novo drug design algorithms for systematic and rational exploration of chemical space [13,14,15] and quantitative structure–activity relationship (QSAR) modeling [16] have been considered promising and useful cheminformatics tools to efficiently broaden our horizons with less experimental costs and without the need to exhaustively evaluate as many as 1033 possible drug-like compounds to find the few of interest
Integration of new molecular generators and other features is facilitated by a documented Python application programming interface (API) while quick Graphical user interface (GUI) customization is possible with an extensive library of components implemented with the React. js JavaScript library

Summary

Introduction

Due to significant technological advances in the past decades, the body of knowledge on the effects and roles of small molecules in living organisms has grown tremendously [1, 2]. In this work we present the development of GenUI, a cheminformatics software framework that provides a GUI and APIs for easy use of molecular generators by human experts as well as their integration with existing drug discovery pipelines and other automated processes. The GenUI framework integrates solutions for import, generation, storage and retrieval of compounds, visualization of the created molecular data sets and basic utilities for QSAR modeling.

Results

Conclusion