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Introduction to computational chemistry, in person

Research Skills

Monday, 16 December 2024 to Wednesday, 18 December 2024, 10am - 5pm

Apply 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:

  • Monday 16 December, 10.00 - 17.00 
  • Tuesday 17 December, 10:00 - 17:00 
  • Wednesday 18 December, 10:00 - 17:00 

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).

The course material will be available here:  https://github.com/bigginlab/OxCompBio

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  

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.

 

Booking Instructions

Step-by-step guidelines on how to book a Skills Training course.

How to book

Terms & Conditions

These terms and conditions apply to all MSD Skills training courses attendees.

Read the Terms & Conditions

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Research Practice e-learning courses are available to all research staff and students at the University. You can self-enrol at Research Practice Training.

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Department of Continuing Education offers Graduate School training programme is for Oxford University postgraduate students. For more details see here.