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Using SMOG 2 to simulate complex biomolecular assemblies

Item Type:Article
Title:Using SMOG 2 to simulate complex biomolecular assemblies
Creators Name:Levi, M. and Bandarkar, P. and Yang, H. and Wang, A. and Mohanty, U. and Noel, J.K. and Whitford, P.C.
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.
Keywords:SMOG, Structure-Based Model, Gō-Model, Coarse-Grained Models, Protein Folding
Source:Methods in Molecular Biology
ISSN:1064-3745
Publisher:Springer / Humana Press (U.S.A.)
Volume:2022
Page Range:129-151
Date:2019
Official Publication:https://doi.org/10.1007/978-1-4939-9608-7_6
PubMed:View item in PubMed

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