Introduction to computational chemistry CLASSROOM
Monday, 12 December 2022 to Wednesday, 14 December 2022, 10am - 5pmApply for this course
This MSD Skills course, run by the Department of Biochemistry, is suitable for all postgraduate research students and early career researchers wanting to understand the practical skills needed for effective computational biochemistry.
You are expected to attend three sessions:
12 December @ 10:00 - 17:00 (Python in simulation and docking (including complete intro to python)
13 December @ 10:00 - 17:00 (MD simulation)
14 December @ 10:00 - 13:00 (Docking)
Computational biochemistry is an extremely important and complementary tool to modern structural biology. In this 3 day workshop, you will learn how to use python via a jupyter notebook and how to perform homology modelling, molecular dynamics and small-molecule docking.
Very little prior knowledge of either python or computational biochemistry is needed for this course and advice will be given prior on how to install the required software (all of which is freeware).
The course is divided into four sessions:
- Introduction to python and jupyter notebooks (2-3 hours with 30 min lecture)
- Introduction to homology modelling (2-3 hours with 30 min lecture)
- Introduction to molecular dynamics (4-5 hours including 1 hour lecture)
- Introduction to small-molecule docking (2-3 hours with 20 min lecture)
Each session will commence with a live-lecture designed to provide some necessary background to the practical components. The four sessions are designed to be done semi-independently (so if you are already very familiar with python, then one could omit that session).
At the end of the course, participants will be able to
- Understand some basic python commands and a jupyter notebook
- Understand how homology modelling works and how to go about building quite complex homology models
- Understand how molecular dynamics works and perform a simulation of a soluble protein
- Understand how docking works and how to interpret the results
HOW IT WILL WORK
This course will run in person in the Broadbent Computing Lab in the basement of Biochemistry. We will use the machines in the Broadbent Laboratory.
The course material will be available here: https://github.com/bigginlab/OxCompBio
ATTENDANCE CERTIFICATE ON SURVEY COMPLETION
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Where no cost is indicated in the shopping trolley, no deposit is required. However, more than two consecutive non-attendances or late cancellations without good reason will be logged and may mean you cannot attend any further MSD training that term. Please refer to our Terms and Conditions for further information.