Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

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:

  • Wednesday 13 December, 10.00 - 17.00 (homology modelling)
  • Thursday 14 December, 10:00 - 17:00 (molecular dynamics)
  • Friday 15 December, 10:00 - 17:00 (molecular dynamics ) 


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: 

  1. Introduction to python and jupyter notebooks (2-3 hours with 30 min lecture)
  2. Introduction to homology modelling (2-3 hours with 30 min lecture)
  3. Introduction to molecular dynamics  (4-5 hours including 1 hour lecture)
  4. 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


Maximum 25  



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:



It is now a requirement that you complete the three short questions in the survey you receive after attending the course. Once you have submitted the survey, you will be sent an email with a link to your attendance certificate. This is to ensure we receive the feedback we need to evaluate and improve our courses. Survey results are downloaded and stored anonymously.


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.