Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations

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https://www.sciencedirect.com/science/article/pii/S1877050914003366

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https://doi.org/10.1016/j.procs.2014.05.159
 http://hdl.handle.net/11603/31601

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UMBC Information Systems Department
UMBC Center for Accelerated Real Time Analysis
UMBC Center for Real-time Distributed Sensing and Autonomy
UMBC Computer Science and Electrical Engineering Department
UMBC Data Science
UMBC Joint Center for Earth Systems Technology (JCET)

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https://orcid.org/0000-0002-9933-1170

Date

2014-06-06

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journal articles
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Citation of Original Publication

Ieong, Pek U., Jesper Sørensen, Prasantha L. Vemu, Celia W. Wong, Özlem Demir, Nadya P. Williams, Jianwu Wang, et al. “Progress towards Automated Kepler Scientific Workflows for Computer-Aided Drug Discovery and Molecular Simulations.” Procedia Computer Science, 2014 International Conference on Computational Science, 29 (January 1, 2014): 1745–55. https://doi.org/10.1016/j.procs.2014.05.159.

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Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0 DEED)

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UMBC Big Data Analytics Lab

Abstract

We describe the development of automated workflows that support computed-aided drug discovery (CADD) and molecular dynamics (MD) simulations and are included as part of the National Biomedical Computation Resource (NBCR). The main workflow components include: file-management tasks, ligand force field parameterization, receptor-ligand molecular dynamics (MD) simulations, job submission, serial and parallel execution, and monitoring on relevant high-performance computing (HPC) resources, receptor structural clustering, virtual screening (VS), and statistical analyses of the VS results. The workflows aim to standardize simulation and analysis and promote best practices within the molecular simulation and CADD communities. Each component is developed as a stand-alone workflow, which should allow for easy integration into larger frameworks built suiting user needs, while remaining intuitive and easy to extend.