CCP-Biosim Workshop

Welcome to the CCP-Biosim Workshop on Free Energy Calculation. Please see below for details of our upcoming workshop in molecular simulation.

Slides from the workshop can be downloaded from here (.pptx) or here (.pdf).

 Free energy methods for modelling of protein-ligand interactions 2014


University of Southampton
Highfield Campus, Building 36, Room 2065

Tuesday 25th November 2014

This CCP-Biosim training workshop will introduce non-specialists to the use of free energy methods for modelling protein-ligand interactions and computing free energies of binding. It is aimed at postgraduate students and early-career researchers, and makes use of the ProtoMS software package for Monte Carlo simulation. However, concepts and practical tips will be transferable to any biomolecular simulation methodology and package.

Want to register? Please do so here. Questions? You can contact the organisers here.
Information about how to get to Southampton is available here.

Provisional schedule:

Time Topic
09:30 Arrival and reception 
10:00 Introduction to molecular simulation
Dr Samuel Genheden, University of Southampton
10:15 Exercise 1
Getting started
Basic usage of ProtoMS
10:45 Alchemical free energy calculations
Dr Samuel Genheden, University of Southampton
11:00 Exercise 2
Relative hydration free energies
12:00
Lunch
13:00 Exercise 2 (cont.)
Relative hydration free energies
13:30
Discussion, intro to exercise 3
13:45
 Exercise 3
Relative binding free energies
15:45
Coffee
16:15 Discussion, own projects/extra projects
Ideas and examples here!
16:30 Research talk : "Making the most from alchemical free energy calculations"
Dr Julien Michel, University of Edinburgh 
17:00 Departure

Not taking part in the workshop? The materials above have been designed for use on the Lyceum teaching cluster at the University of Southampton. You might find the ProtoMS setup instructions useful.