Work Description

Title: Equilibrium Path Sampling Data for Two Glycosynthetic Reactions of Thermatoga maratima Alpha-L-Fucosidase D224G Open Access Deposited

http://creativecommons.org/licenses/by/4.0/
Attribute Value
Methodology
  • This data concerns equilibrium path sampling, which is a method of measuring the free energy along a specified reaction coordinate by dividing the reaction coordinate into discrete windows and sampling the relative frequencies with which unbiased simulations visit different parts of each window. The data was collected using the proprietary, open-source software ATESA:  https://github.com/team-mayes/atesa
Description
  • This project aimed to discover and analyze the molecular mechanism of synthesis of two particular fucosylated oligosaccharide products in a mutant enzyme, Thermatoga maratima Alpha-L-Fucosidase D224G, whose wild type performs the opposite reaction (cleavage of fucosyl glycosidic bonds). Discovery of the mechanism was performed using an unbiased simulations method known as aimless shooting, whereas analysis of the mechanism in terms of the energy profile was performed using a separate method known as equilibrium path sampling. The data here concerns the latter method.

  • The contents of the atesa_master.zip are the ATESA GitHub project. A Python program for automating transition path sampling with aimless shooting using Amber.  https://github.com/team-mayes/atesa
Creator
Depositor
  • tburgin@umich.edu
Contact information
Discipline
Funding agency
  • National Science Foundation (NSF)
Keyword
Date coverage
  • 2018-05-28 to 2018-10-24
Citations to related material
  • 10.1039/C8RE00240A
Resource type
Last modified
  • 08/21/2019
Published
  • 07/19/2019
Language
License
To Cite this Work:
Burgin, T., Mayes, H. (2019). Equilibrium Path Sampling Data for Two Glycosynthetic Reactions of Thermatoga maratima Alpha-L-Fucosidase D224G [Data set]. University of Michigan - Deep Blue.

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