Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations

Pek U Ieong; Jesper Sørensen; Prasantha L Vemu; Celia W Wong; Özlem Demir; Nadya P Williams; Jianwu Wang; Daniel Crawl; Robert V Swift; Robert D Malmstrom; Ilkay Altintas; Rommie E Amaro

doi:10.1016/j.procs.2014.05.159

Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations

Procedia Comput Sci. 2014:29:1745-1755. doi: 10.1016/j.procs.2014.05.159.

Authors

Pek U Ieong^{1

2}, Jesper Sørensen¹, Prasantha L Vemu¹, Celia W Wong¹, Özlem Demir¹, Nadya P Williams^{3

2}, Jianwu Wang³, Daniel Crawl^{3

2}, Robert V Swift¹, Robert D Malmstrom^{1

2}, Ilkay Altintas^{3

2}, Rommie E Amaro^{1

2}

Affiliations

¹ Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA.
² National Biomedical Computation Resource, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA.
³ San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA.

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 Computational Resource (NBCR). The main workflow components include: file-management tasks, ligand force field parameterization, receptor-ligand molecular dynamics (MD) simulations, job submission 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 allows easy integration into larger frameworks built to suit user needs, while remaining intuitive and easy to extend.

Keywords: Scientific workflows; big data reduction; ligand parameterization; molecular simulation; relaxed complex scheme; small molecule docking; structural clustering; web services.

Abstract

Grants and funding