S. Bray, Albert Ludwigs University Freiburg
Service center: RNA Bioinformatics Center – RBC
The ChemicalToolbox is a set of tools to perform cheminformatics data analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tasks for downloading, filtering, visualization and simulation of small molecules and proteins. Based on this work, we provide workflows which demonstrate the typical use-cases, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model. These workflows can be modified and combined flexibly, together with the many other tools available, to fit the needs of a particular project.
In this project, we have used the ChemicalTool Box suite which is integrated in the European Galaxy instance for protein-ligand docking to identify potentially inhibitory compounds that can bind to the main protease Mpro of the Coronavirus (SARS-CoV-2 Mpro) and can be used to control viral proliferation. This work analysed over 40,000 compounds considered to be likely to bind to one of the SARS-CoV-2 proteases. From them, 500 high-scoring compounds have been identified and will undergo testing soon. Together with other research partners we joined forces to construct and execute a Galaxy workflow for performing and evaluating molecular docking on a massive scale. All workflows, training material and results are publically available on a specific Galaxy website.
For further information visit: https://covid19.galaxyproject.org/cheminformatics/Histories
To access the Galaxy tutorial: https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html
Figure: Structure of MPro, with a fragment bound. Click to view in NGL. (Rose et al. 2018).