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SNP2SIM: A modular workflow for standardizing molecular simulation and functional analysis of protein variants

By Matthew D McCoy, Vikram Shivakumar, Sridhar Nimmagadda, Mohsin Saleet Jafri, Subha Madhavan

Posted 30 Oct 2018
bioRxiv DOI: 10.1101/457192 (published DOI: 10.1186/s12859-019-2774-9)

Molecular simulations are used to provide insight into protein structure and function, and have the potential to provide important context when predicting the impact of sequence variation on protein function. In addition to understanding molecular mechanisms and interactions on the atomic scale, translational applications of those approaches include drug screening, development of novel molecular therapies, and treatment planning when selecting targeted therapies. Supporting the continued development of these applications, we have developed the SNP2SIM workflow generates reproducible molecular dynamics and molecular docking simulations for downstream functional variant analysis. Three modules execute molecular dynamics simulations of solvated protein variant structures, analyze the resulting trajectories for unique structural conformations, and bind small molecule ligands to representative variant scaffolds. In addition to availability as a command line workflow, SNP2SIM modules are also available as individual apps on the Seven Bridges Cancer Genomics Cloud.

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