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SMOG 2 and OpenSMOG: extending the limits of structure-based models

Item Type:Article
Title:SMOG 2 and OpenSMOG: extending the limits of structure-based models
Creators Name:de Oliveira, A.B. and Contessoto, V.G. and Hassan, A. and Byju, S. and Wang, A. and Wang, Y. and Dodero-Rojas, E. and Mohanty, U. and Noel, J.K. and Onuchic, J.N. and Whitford, P.C.
Abstract:Applying simulations with structure-based (Gõ-like) models has proven to be an effective strategy for investigating the factors that control biomolecular dynamics. The common element of these models is that some (or all) of the intra/inter-molecular interactions are explicitly defined to stabilize an experimentally-determined structure. To facilitate the development and application of this broad class of models, we previously released the SMOG 2 software package. This suite allows one to easily customize and distribute structure-based (i.e. SMOG) models for any type of polymer-ligand system. The force fields generated by SMOG 2 may then be used to perform simulations in highly-optimized MD packages, such as Gromacs, NAMD, LAMMPS and OpenMM. Here, we describe extensions to the software and demonstrate the capabilities of the most recent version (SMOG v2.4.2). Changes include new tools that aid user-defined customization of force fields, as well as an interface with the OpenMM simulation libraries (OpenSMOG v1.1.0). The OpenSMOG module allows for arbitrary user-defined contact potentials and non-bonded potentials to be employed in SMOG models, without source-code modifications. To illustrate the utility of these advances, we present applications to systems with millions of atoms, long polymers and explicit ions, as well as models that include non-structure-based (e.g. AMBER-based) energetic terms. Examples include large-scale rearrangements of the SARS-CoV-2 Spike protein, the HIV-1 capsid with explicit ions, and crystallographic lattices of ribosomes and proteins. In summary, SMOG 2 and OpenSMOG provide robust support for researchers who seek to develop and apply structure-based models to large and/or intricate biomolecular systems.
Keywords:COVID-19, Coronavirus Spike Glycoprotein, Molecular Dynamics Simulation, Molecular Models, Protein Conformation, Proteins, Ribosomes, SARS-CoV-2, Software, Animals
Source:Protein Science
ISSN:0961-8368
Publisher:Wiley
Volume:31
Number:1
Page Range:158-172
Date:January 2022
Official Publication:https://doi.org/10.1002/pro.4209
PubMed:View item in PubMed

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