AutoDock Gateway for Molecular Docking Simulations in Cloud Systems

Farkas, Zoltán; Kacsuk, Péter; Kiss, Tamás; Borsody, P.; Hajnal, Ákos; Balaskó, Ákos; Karóczkai, Krisztián

doi:10.1201/b18021-10

Cited by 6 publications

(6 citation statements)

References 5 publications

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“…One example of a scientific workflow is WS-PGRADE and the gUSE services [36][37][38] which have been used to run docking experiments using various DCIs, such as clouds [39], grids [40] or HPC clusters [41]. In the latter example, interviews with one expert biochemist have been conducted to gather user requirements and implement a docking gateway.…”

Section: Related Workmentioning

confidence: 99%

Building Science Gateways for Analysing Molecular Docking Results Using a Generic Framework and Methodology

et al. 2020

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Molecular docking and virtual screening experiments require large computational and data resources and high-level user interfaces in the form of science gateways. While science gateways supporting such experiments are relatively common, there is a clearly identified need to design and implement more complex environments for further analysis of docking results. This paper describes a generic framework and a related methodology that supports the efficient development of such environments. The framework is modular enabling the reuse of already existing components. The methodology, which proposes three techniques that the development team can use, is agile and encourages active participation of end-users. Based on the framework and methodology, two prototype implementations of science-gateway-based docking environments are presented and evaluated. The first system recommends a receptor-ligand pair for the next docking experiment, and the second filters docking results based on ligand properties.

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Section: Related Workmentioning

confidence: 99%

Building Science Gateways for Analysing Molecular Docking Results Using a Generic Framework and Methodology

et al. 2020

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“…A fourth example uses WS-PGRADE/gUSE technology and the CloudBroker Platform to enable docking with AutoDock4 or AutoDock Vina on various clouds [20]. The user can upload input files, run pre-defined workflows and download the results.…”

Section: Related Workmentioning

confidence: 99%

“…All these attempts provided their own restricted GUI for running the simulations, and required a separate environment for pre-processing or post-processing. They were, with the exception of [20], focusing on one specific cloud computing infrastructure. In comparison, the approach suggested in this article, enables scientists to use the GUI of a popular domain-specific desktop application they are familiar with (Raccoon2).…”

Section: Related Workmentioning

confidence: 99%

“…Krüger et al (2014) [7] provide workflows for docking, they store the docking results using a custom-made implementation on a distributed file system, and further analyse the docking results by re-scoring or visualising them. Other examples include [20] and [6].…”

Section: Related Workmentioning

confidence: 99%

“…Extensive research in docking has produced many excellent systems. Some of them merely provide an environment to conduct the docking simulations [6,18,20,26], while others provide additional methods for the user to analyse their results [7,8,10,[23][24][25]. However, in all cases it is only the user's own results that are available for analysis.…”

Section: Related Workmentioning

confidence: 99%

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

Temelkovski

Kiss

Terstyánszky

et al. 2019

Future Generation Computer Systems

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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 domainspecific 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.

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