RT Journal Article
SR Electronic
T1 Using SMOG 2 to simulate complex biomolecular assemblies
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 371617
DO 10.1101/371617
A1 Mariana Levi
A1 Prasad Bandarkar
A1 Huan Yang
A1 Ailun Wang
A1 Udayan Mohanty
A1 Jeffrey K. Noel
A1 Paul C. Whitford
YR 2018
UL http://biorxiv.org/content/early/2018/07/18/371617.abstract
AB 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 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.