Extending molecular docking desktop applications with cloud computing support and analysis of results

Abstract Structure-based virtual screening simulations, which are often used in drug discovery, can be very computationally demanding. This is why user-friendly domain-specific web or desktop applications that enable running simulations on powerful computing infrastructures have been created. This article investigates how domain-specific desktop applications can be extended to use cloud computing and how they can be part of scenarios that require sharing and analysing previous molecular docking results. A generic approach based on interviews with scientists and analysis of existing systems is proposed. A proof of concept is implemented using the Raccoon2 desktop application for virtual screening, WS-PGRADE workflows, gUSE services with the CloudBroker Platform, the structural alignment tool DeepAlign, and the ligand similarity tool LIGSIFT. The presented analysis illustrates that this approach of extending a domain-specific desktop application can use different types of clouds, thus facilitating the execution of virtual screening simulations by life scientists without requiring them to abandon their favourite desktop environment and providing them resources without major capital investment. It also shows that storing and sharing molecular docking results can produce additional conclusions such as viewing similar docking input files for verification or learning.