A collection of scripts written for use with different computational biology/chemistry packages throughout my PhD.
pdb_download.sh (2023/10/11)
Download a list of PDB files using a text file containing one 4-character PDB code on each line.
align_pdb.py (2024/02/02)
Align a list of PDB files to a reference structure using PyMOL (Schrödinger, Inc.).
split.py (2023/01/23)
Determine the number of monovalent salt ions are required for an explicit solvent molecular dynamics (MD) simulation using the SPLIT method. Method created by Dr. Matias Machado (2020).
Designed for use with LEaP (AmberTools).
amber2csm.py (2024/01/15)
Re-format pdb files from MD simulations using AMBER and GLYCAM force fields via cpptraj (AmberTools). 3-letter sugar residue codes are renamed to match those found on the Protein Data Bank (PDB) for compatibility with CSM-carbohydrate, a webserver predicting protein-carbohydrate binding affinity (Nguyen et al. 2022).
fixatomnum.py (2024/01/19)
Fix the atom numbering (columns 7-11) for PDB files that have had new atoms added to them using pdb4amber (AmberTools; Case et al. 2023), or MolProbity (Williams et al. 2017).
adv_config.py (2023/09/29)
Generates a template config file for use with AutoDock Vina/Vina-Carb using the grid dimensions from an grid AutoDockTools grid dimensions file.
read_pressure.py (2023/12/15)
Measure and record the pressure within the current Manchester Future BRH flow chemistry setup using Fluigent Microfluidic In-Line Pressure Sensor (IPS). More information about the IPS can be found here: https://www.fluigent.com/research/instruments/sensors/pressure-unit/
Requires the Fluigent SDK.