CCPBioSim Training Week - Day 4: Monte Carlo Methods for Biomodelling

Event Date/s: Thursday 09 June 2016



2.11 Merchant Venturers Building, Department of Electrical and Electronic Engineering, Woodland Road, Bristol BS8 1UB.

Travel directions are at


Please note: Research talks will take place in Lecture Theatre 3 in the School of Chemistry, Cantocks Close, BS8 1TS.



There is no fee for registering for this workshop. However, participants are responsible for arranging and the costs of their own travel and accommodation. We have provided a list of recommended places to stay below, should you need overnight accommodation. To register for this workshop day only please follow this link. Delegates wishing to attend multiple workshop days during this training week must register for those days separately. 


Please note: that is this is the first time that you have used the STFC event registration system then you will need to create an account before you can register for any of the courses.



10.00 - 4.00pm    Monte Carlo Methods for Biomodelling

Instructor: Dr Christopher Woods (see:

The workshop will comprise the below three parts, which can be worked through at your own pace.

Part 1 - Introduction to Monte Carlo

Part 2 - Monte Carlo Methods for Biomodelling

Part 3 - LigandSwap - using Monte Carlo to calculate relative binding free energies


4.30pm - 5.30pm        Research talk: Dr Christopher Woods - "Drug design using Monte Carlo - How black should the box be?"

One of the grand challenges for computational biomodelling is the creation of "black box" tools that can fully automate rational drug design. A lot of progress has been made towards this goal, e.g. the development of tools to automate simulation setup, the creation of new Monte Carlo methods for calculating binding affinities, methods to automatically submit calculations to HPC computers, and the availability of new visualisation tools for analysis. This talk will discuss some of this progress, and will raise the questions of what technologies need to be developed to achieve this goal, and how fully automatic the drug design tool should be?


Aimed at: PhD students and Postdocs that are interested in learning more about Monte Carlo methods for molecular modelling.


Requirements: A basic knowledge of the Linux command line, and a basic knowledge of Python (e.g. as gained from "Beginning Python",



The programme consists of three parts, all based on a self-guided workshop that is available here - In part 1, you will learn about the basics of Monte Carlo, how it works, the meaning of different control variables, and how a Monte Carlo program is implemented. In part 2, you will learn how to put this together to simulate biomolecules, such as proteins. Finally, in part 3, you will learn how to use Monte Carlo to run simulations that calculate protein-ligand binding free energies.


Accommodation is NOT included with your registration for this event. Should you require accommodation (e.g. when attending multiple one-day events), you should make your own arrangements. We can recommend the following:

Clifton House - website - 0117 973 5407

Premier Inn, Haymarket Bristol - website  - 0117 910 0600

Victoria Square Hotel - website - 0117 973 9058

Berkeley Square Hotel - website - 0117 925 4000



For queries related to this days workshop contact:

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For more general workshop queries, contact:

Marc van der Kamp: This email address is being protected from spambots. You need JavaScript enabled to view it.