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Developing science gateways for drug discovery in a grid environment

, , , , , ,
1 Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engeneering Department), Universidad Católica San Antonio (UCAM), Murcia, Spain
2 The National Organization for Educational Testing (NOET), Ministry of Science, Research and Technology, Tehran, Iran
3 School of Biological Science, Institute for Research in Fundamental Science (IPM), Tehran, Iran
4 Faculty of Computer Systems and Software Engineering, University Malaysia Pahang, Gambang, Pahang, Malaysia
5 Department of Information Engineering, Graduate School of Engineering, Hiroshima University, Hiroshima, Japan
6 Department of Computer Science and Engineering and Center for Research Computing, University of Notre Dame, Notre Dame, IN, USA
DOI
10.7287/peerj.preprints.1245v1
Published
Accepted
Subject Areas
Bioinformatics, Computational Biology, Human-Computer Interaction, Distributed and Parallel Computing
Keywords
Virtual Screening, FlexScreen, Science gateways, Drug Discovery, High Performance Computing
Copyright
© 2015 Pérez-Sánchez et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Pérez-Sánchez H, Rezaei Tabar V, Mezhuyev V, Man D, Peña-García JJ, den-Haan H, Gesing S. 2015. Developing science gateways for drug discovery in a grid environment. PeerJ PrePrints 3:e1245v1

Abstract

Methods for in-silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life-sciences with a convenient tool for high-throughput virtual screening (HTVS) on distributed computing resources. To this end, we recently integrated the biophysics-based drug screening program FlexScreen into a service applicable for large-scale parallel screening and reusable in the context of scientific workflows. Our implementation, based on Pipeline Pilot and Simple Object Access Protocol (SOAP) provides an easy-to-use graphical user interface to construct complex workflows which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.

Author Comment

This is a submission to PeerJ Computer Science for review.

Additional Information

Competing Interests

Sandra Gesing is an Academic Editor for PeerJ Computer Science.

Author Contributions

Horacio Pérez-Sánchez performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Vahid Rezaei Tabar performed the experiments, analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.

Vitaliy Mezhuyev performed the experiments, analyzed the data, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Duhu Man performed the experiments, analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.

Jorge Jpg Peña-García performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Helena den-Haan performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Sandra Gesing conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Funding

This work was partially supported by the Fundación Séneca del Centro de Coordinación de la Investigación de la Región de Murcia under Project 18946/JLI/13 and by the Nils Coordinated Mobility under grant 012-ABEL-CM-2014A, in part financed by the European Regional Development Fund (ERDF). This work was partially supported by the computing facilities of Extremadura Research Centre for Advanced Technologies (CETA-CIEMAT), funded by the European Regional Development Fund (ERDF). CETA-CIEMAT belongs to CIEMAT and the Government of Spain. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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