Oct 30, 2018

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

BioRxiv : the Preprint Server for Biology
Matthew D McCoySubha Madhavan

Abstract

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.

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

Molecular Dynamics
Molecular Docking Simulation
Protein Function
Genomics
Binding (Molecular Function)
Structure
Simulation
Analysis
Physiological Aspects
Genetic Translation Process

About this Paper

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

© 2020 Meta ULC. All rights reserved