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Using SMOG 2 to Simulate Complex Biomolecular Assemblies

  • Mariana Levi
  • Prasad Bandarkar
  • Huan Yang
  • Ailun Wang
  • Udayan Mohanty
  • Jeffrey K. Noel
  • Paul C. WhitfordEmail author
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Part of the Methods in Molecular Biology book series (MIMB, volume 2022)

Abstract

Over the last 20 years, the application of structure-based (Gō-like) models has ranged from protein folding with coarse-grained models to all-atom representations of large-scale molecular assemblies. While there are many variants that may be employed, the common feature of these models is that some (or all) of the stabilizing energetic interactions are defined based on the knowledge of a particular experimentally obtained conformation. With the generality of this approach, there was a need for a versatile computational platform for designing and implementing this class of models. To this end, the SMOG 2 software package provides an easy-to-use interface, where the user has full control of the model parameters. This software allows the user to edit XML-formatted files in order to provide definitions of new structure-based models. SMOG 2 reads these “template” files and maps the interactions onto specific structures, which are provided in PDB format. The force field files produced by SMOG 2 may then be used to perform simulations with a variety of popular molecular dynamics suites. In this chapter, we describe some of the key features of the SMOG 2 package, while providing examples and strategies for applying these techniques to complex (often large-scale) molecular assemblies, such as the ribosome.

Key words

SMOG Structure-based model Gō-model Coarse-grained models Protein folding 

Notes

Acknowledgements

This work was supported in part by an NSF CAREER Award (Grant MCB-1350312). JKN is a Humboldt Postdoctoral Fellow. UM acknowledges support as a John Simon Guggenheim Memorial Foundation fellowship. We acknowledge generous support provided by Northeastern University Discovery Cluster.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Mariana Levi
    • 1
  • Prasad Bandarkar
    • 1
  • Huan Yang
    • 1
  • Ailun Wang
    • 2
  • Udayan Mohanty
    • 2
  • Jeffrey K. Noel
    • 3
  • Paul C. Whitford
    • 1
    Email author
  1. 1.Department of PhysicsNortheastern UniversityBostonUSA
  2. 2.Department of ChemistryBoston CollegeChestnut HillUSA
  3. 3.Max Delbrueck Center for Molecular MedicineKristallographieBerlinGermany

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