Introduction to computational chemistry CLASSROOM

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) 

COURSE AIM

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).

COURSE DESCRIPTION

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).

COURSE OBJECTIVES

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

PARTICIPANT NUMBERS

Maximum 25  

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

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.

PLEASE NOTE

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.