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Performance Studies on Distributed Virtual Screening
Joint Authors
Herres-Pawlis, Sonja
Kohlbacher, Oliver
Grunzke, Richard
de la Garza, Luis
Gesing, Sandra
Hoffmann, Alexander
Nagel, Wolfgang E.
Krüger, Jens
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-7, 7 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-06-17
Country of Publication
Egypt
No. of Pages
7
Main Subjects
Abstract EN
Virtual high-throughput screening (vHTS) is an invaluable method in modern drug discovery.
It permits screening large datasets or databases of chemical structures for those structures binding possibly to a drug target.
Virtual screening is typically performed by docking code, which often runs sequentially.
Processing of huge vHTS datasets can be parallelized by chunking the data because individual docking runs are independent of each other.
The goal of this work is to find an optimal splitting maximizing the speedup while considering overhead and available cores on Distributed Computing Infrastructures (DCIs).
We have conducted thorough performance studies accounting not only for the runtime of the docking itself, but also for structure preparation.
Performance studies were conducted via the workflow-enabled science gateway MoSGrid (Molecular Simulation Grid).
As input we used benchmark datasets for protein kinases.
Our performance studies show that docking workflows can be made to scale almost linearly up to 500 concurrent processes distributed even over large DCIs, thus accelerating vHTS campaigns significantly.
American Psychological Association (APA)
Krüger, Jens& Grunzke, Richard& Herres-Pawlis, Sonja& Hoffmann, Alexander& de la Garza, Luis& Kohlbacher, Oliver…[et al.]. 2014. Performance Studies on Distributed Virtual Screening. BioMed Research International،Vol. 2014, no. 2014, pp.1-7.
https://search.emarefa.net/detail/BIM-486002
Modern Language Association (MLA)
Krüger, Jens…[et al.]. Performance Studies on Distributed Virtual Screening. BioMed Research International No. 2014 (2014), pp.1-7.
https://search.emarefa.net/detail/BIM-486002
American Medical Association (AMA)
Krüger, Jens& Grunzke, Richard& Herres-Pawlis, Sonja& Hoffmann, Alexander& de la Garza, Luis& Kohlbacher, Oliver…[et al.]. Performance Studies on Distributed Virtual Screening. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-7.
https://search.emarefa.net/detail/BIM-486002
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-486002