Molecular Modelling of Covalent Inhibition of Bruton’s Tyrosine Kinase by Cyanoacrylamides
Project Details
- Author: Jonathan Yik Chang Ting
- Student ID: 44254124
- Supervisors: Associate Professor Elizabeth Krenske, Professor Alan Mark, Dr Martin Stroet
- Institution: University of Queensland
- Organisation: School of Chemistry and Molecular Biosciences
- Programme: Bachelor of Advanced Science (Honours)
- Course: Honours in Chemistry (CHEM6511)
- Year: 2019
Project Phases
Quantum Mechanical Calculations
- QM directory contains the Python files written for various purposes related to the QM calculation phase of the project:
Files in run_gaussian directory are for the automation of generation of QM calculation input files and job submission files, grouping of files with same names, and QM data tabulation. Files in Csearch directory are some functions I used while trying to come up with ways to explain the conformaitonal searching phase of the project for my Honours seminar. Files in visualG directory are either for plotting of energy profiles for Cross-Conjugation project (a side project) or the linear regression analysis of certain molecular properties. The data are stored in plot_config.py while the plotting codes are mainly written in plot_fig.py. Figures generated from the analysis on data generated using Combination G and I were stored in the respective directories. calculation.py was used for interconversion between kinetics and thermodynamics parameters during the early phase of the project.
- QM_Gaussian directory contains the same files as QM/run_gaussian. It is generalised for the usage of others who wish to automate some tasks involved in the conformational searching phase of the QM calculations of flexible molecules using Gaussian.
Molecular Dynamics Simulations
- MD directory contains the Python files written for the analysis of simulation trajectories of BTK inhibited by different inhibitors.