READ ME File For 'Dataset in support of the thesis 'Investigating the conformational dynamics of the Major Histocompatibility Complex class I'

Dataset DOI: https://doi.org/10.5258/SOTON/D2922

ReadMe Author: Steven Turner, Andy Van Hateren, Jon W. Essex, University of Southampton.



Description:
This folder contains all datasets (or parameters for recreation of datasets in the case for large simulations) seperated by relevant chapter.

Chapter 3
	Data:
		A0201_pepsin: DynamX formatted output for A0201 pepsin digest HDX results (.xtc file) & SDS-PAGE labelled image (SDS-PAGE).
		B4402vsW147A: DynamX formatted output for B4405 and B4405_W147A pepsin digest HDX results (.txt file) and python plotting scripts.
		PhosB_Tryp_Native: DynamX formatted output for PhosB with native and Trypsin digest (.DnX file) and python plotting scripts.
	PfactCorpy:
		Custom python module for analysis of DynamX deuterium uptake files.
Chapter 4
	Analysis Scripts:
		Python and bash scripts used for simulation analysis in Chapter 4.
	Simulation Scripts:
		Input structures (.pdb), simulation starting structures (.gro), simulation topologies (.top), simulation running scripts (.slurm) and simulation parameter files (.mdp) for each simulation in Chapter 4.
Chapter 5
	FP_analysis:
		Python scripts and module for the analysis of Fluorescence Polarisation data.
	Sequence Logo:
		Python scripts and input data (.msf) for the generation of MHC-I sequence logos.
	Simulations:
		Input structures (.pdb), simulation starting structures (.gro), simulation topologies (.top), simulation running scripts (.slurm) and simulation parameter files (.mdp) for each simulation in Chapter 5.
Chapter 6
	Simulation:
		Input structures (.pdb), simulation starting structures (.gro), simulation topologies (.top), simulation running scripts (.slurm) and simulation parameter files (.mdp) for each simulation in Chapter 6. Additional python analysis scripts included.
Chapter 7
	Simulations:
		Input structures (.pdb), simulation running scripts (.slurm and .py) for each simulation in Chapter 7. Simulation parameter files (.mdp) provided in mdpfiles subdirectory. GaMD reweighting data for alanine dipeptide included in Diala_GaMD_Data subdirectory (.txt).

Dataset available under a CC BY 4.0 licence

Publisher: University of Southampton, U.K.

Date: April 2024