Training Week 2022
Monday 19 September 2022, 09:00 - 17:00


Because of the bank holiday in the UK on 19 September 2022, the Monday workshops (Basic and Advanced Python) have been cancelled; the other workshops remain as scheduled. The training week will begin on Tuesday 20 September with the BioSimSpace workshop.

This week long training event includes a variety of different workshops. We recommend that where possible you attend all of the workshops, because insight into a broad range of tools can be very helpful.


This is a hybrid event - the in person delegates will be at the University of Leeds (UK) and the online programme will be via Zoom. Links or room details will be sent to registered partipants closer to the event.


Please apply for this workshop on the event booking site (link here). When you complete the registration form you will be asked to explain why this training would be helpful to you in less than 300 words. We will use this information to assign places at the workshop if we are over-subscribed.

Application Deadline: 15 August 2022.

Notification for Sucessful Applicants: 22 August 2022.

Space Available - 30 in person / 20 online.

Fee - There is no cost, this covers the workshops and lunch for in person delegates (accommodation, breakfast, and dinner are not included).

Programme (Subject to change)

9:00 – 12:00, Monday 19 September
Topic: Basic Python
Prerequisites: none

14:00 – 17:00, Monday 19 September
Topic: Advanced Python
Prerequisites: basic python

9:00 – 12:00, Tuesday 20 September
Topic: BioSimSpace
Description: This workshop will introduce non-specialists to the use of alchemical free energy methods to compute protein-ligand binding free energies. Brief lectures will introduce the key concepts of relative and absolute binding free energy calculations. Hands-on exercises will illustrate how the BioSimSpace software library may be used to perform such calculations with a variety of software implementations. The tutorial will also highlight how BioSimSpace may be extended to support new functionality.
Prerequisites: Python, knowledge of atomistic simulations.

14:30 – 17:30, Tuesday 20 September
Topic: ProDy
Prerequisites: install ProDy (instructions will be send to registered participants 1 week before)

9:00 – 12:00, Wednesday 21 September
Topic: Cresset Software
Description: Flare is a comprehensive platform for ligand-based and structure-based molecule design. In this workshop you will learn how to enhance high-throughput computational chemistry using the Flare Python API. Starting with short code snippets, and moving to more advanced scripts, we will demonstrate how to use Python code within Flare to set up and run large-scale experiments efficiently. All of Flare's scientific features are fully accessible via the Flare Python API, as well as popular tools used in computational chemistry and cheminformatics, such as the RDKit. With the help of Python notebooks, you will learn how to automate routine processes like protein preparation and docking; modify Flare’s interface to suit your needs; and export detailed, high-resolution graphical representations of your data. Programming is a highly beneficial skill in modern science, regardless of discipline, therefore, we encourage participants of all skill levels to come and learn about the Flare Python API.

15:00-18:00, Wednesday 21 September
Topic: AutoDock

9:00 – 12:00, Thursday 22 September
Topic: oxDNA
Prerequisites: knowledge of MD, command line, and C++ complier

14:00 – 17:00, Thursday 22 September
Topic: QM/MM
Description: The training workshop will introduce non-specialists to the use of combined quantum mechanics/molecular mechanics (QM/MM) methods for modelling enzyme-catalysed reaction mechanisms. Concepts and techniques of QM/MM reaction modelling will be explained through hands-on exercises. During the tutorial, each participant will generate and analyse a free energy profile and a potential energy profile for the reaction catalysed by chorismate mutase.
Prerequisites: Knowledge of atomistic MD simulations.

9:00 – 17:00, Friday 23 September
Topic: BigDFT


No accommodation is provided.


For further information or queries, contact:

Sarah Fegan: This email address is being protected from spambots. You need JavaScript enabled to view it. or Pijro Johnson: This email address is being protected from spambots. You need JavaScript enabled to view it.