READ ME File For 'Antibody REST2 Dataset'

Dataset DOI: 10.5258/SOTON/D2191

ReadMe Author: Mabel Wong, University of Southampton 0000-0003-3752-8979

This dataset supports the thesis entitled 'The Role of Hydration and Flexibility in Computational Antibody Design' 
AWARDED BY: Univeristy of Southampton
DATE OF AWARD: 2022

DESCRIPTION OF THE DATA

This dataset contains the following directories:
- antiobr_rest2_tests: .tpr files for simulations to optimise REST2 protocol 
- apo_tprs: antibody-only .tpr files required to regenerate the REST2 dataset and GCMC/MD simulations.
- holo_tprs: antibody-antigen .tpr files required to regenerate the REST2 dataset and GCMC/MD simulations.
- scripts: scripts for GCMC/MD simulations and analysis scripts and instructions to analyse the data using methods described in the thesis

Software requirements
- To regenerate dataset:  GROMACS 2018.2 or later patched with PLUMED, grand 1.0.1 or later
- Dataset analysis: python 3 (see scripts for required modules), DASH (or mDASH), GROMACS 2018.2 or later


Date of data collection: January 2019 - July 2021

Information about geographic location of data collection: Southampton Iridis 5 cluster, ARCHER (all UK) 

Related projects/Funders:
BBSRC (grant no. BB/P504713/1)
EPSRC (grant no. EP/R029407/1) via the UK HECBioSim
UCB

Related publication: None as of 21/04/2022


Date that the file was created: April, 2022

--------------