READ ME File For 'Thesis Chapters 5 and 6 Datasets'

Dataset DOI: 10.5258/SOTON/D2296

ReadMe Author: Khaled Abdel-Maksoud, University of Southampton ORCID 0000-0002-6029-4966

This dataset supports the thesis entitled Conformational 
Enhanced Sampling: The study and development of accelerated sampling algorithms for classical biomolecular dynamics
AWARDED BY: Univeristy of Southampton
DATE OF AWARD: 2022

DESCRIPTION OF THE DATA
This dataset supports the results chapters (Chapters 5 and 6) of the aformentioned thesis. The dataset entry is comprised of a set of compressed tarballs (.tar.gz) format containing datafiles, pickled data dictionaries and NumPy array files that can be used to reproduce the analysis and plots presented in these chapters.

In order to extract these files, the following command can be executed in any bash/sh terminal:-

tar -xvzf <name of tarball file> .

This dataset contains:

tchap5_data1.tar.gz - Contains validation model data for the quantitative metric workflow for CV-based enhanced sampling methods – 2D NT/WTMetaD of alanine dipeptide, two state (folded + unfolded) models of three model peptides presented in Chapter 5 of the thesis

tchap5_data2.tar.gz - Contains bias convergence data, CV cluster data and associated phase space similarity data for NT/WTMetaD simulations of TrpCage folding presented in Chapter 5 of the thesis

tchap6_data1.tar.gz - Contains a list of PDB files considered in empirical analysis of main protease dyad conformations vs protease activity presented in Chapter 6 of the thesis 

tchap6_data2.tar.gz - Contains MetaD CV data for His41 imidazole rotation induced inhibition of the SARS-CoV 2 main protease via His41-Cys145 dyad disruption presented in Chapter 6 of the thesis

Date of data collection: 

Information about geographic location of data collection: 

Licence:
CC-BY

Related projects/Funders:
EPSRC - Theory and Modelling in Chemical Sciences (EP/L015722/1)

Related publication:
None


Date that the file was created: July, 2022