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Go-Kit: A Tool To Enable Energy Landscape Exploration of Proteins.

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Neelamraju, Sridhar 
Wales, David J 
Gosavi, Shachi 

Abstract

Coarse-grained Go̅-like models, based on the principle of minimal frustration, provide valuable insight into fundamental questions in the field of protein folding and dynamics. In conjunction with commonly used molecular dynamics (MD) simulations, energy landscape exploration methods like discrete path sampling (DPS) with Go̅-like models can provide quantitative details of the thermodynamics and kinetics of proteins. Here we present Go-kit, a software that facilitates the setup of MD and DPS simulations of several flavors of Go̅-like models. Go-kit is designed for use with MD (GROMACS) and DPS (PATHSAMPLE) simulation engines that are open source. The Go-kit code is written in python2.7 and is also open source. A case study for the ribosomal protein S6 is discussed to illustrate the utility of the software, which is available at https://github.com/gokit1/gokit .

Description

Keywords

Bacterial Proteins, Kinetics, Molecular Dynamics Simulation, Protein Conformation, Protein Folding, Proteins, Ribosomal Protein S6, Software, Thermodynamics, Thermus thermophilus

Journal Title

J Chem Inf Model

Conference Name

Journal ISSN

1549-9596
1549-960X

Volume Title

59

Publisher

American Chemical Society (ACS)

Rights

All rights reserved
Sponsorship
Engineering and Physical Sciences Research Council (EP/N035003/1)
epsrc