CCPBioSim Training Week - Day 1: Enlighten: Tools for enzyme-ligand modelling

Event Date/s: Monday 06 June 2016

 

This tutorial workshop is made possible by support from BBSRC.

 

The course material can be found here

 

Venue

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

Travel directions are at http://www.bristol.ac.uk/maps/directions/

 

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

 

Registration

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.

 

Programme

10.30 - 4.00pm  Tutorial and feedback session on Enlighten (for experimentalists/protein crystallographers) 

Instructors: Dr Marc van der Kamp & Dr Kara Ranaghan

 

4.30pm - 5.30pm        Research talk

Dr Marc van der Kamp - "In silico enzyme activity screening: applications in antibiotic resistance and evaluation of biocatalysts"

Hybrid quantum mechanical / molecular mechanical (QM/MM) modelling of enzyme reactions has been used extensively to reveal the detailed mechanisms of many enzymes. Application of QM/MM as a tool for in silico screening of enzyme activity is still limited, however. Here, I will first show how QM/MM umbrella sampling can be used to predict whether a β-lactamase can break down particular carbapenems (‘antibiotics of last resort’). Then, I will indicate how automated protocols, such as those available from Enlighten, can be used to investigate enzyme activity and selectivity in two enzymes that can be used as biocatalysts. These examples highlight the potential of automated simulation protocols and QM/MM modelling to generate hypotheses and perform activity screening of enzyme variants.

 

Aimed at: Experimental biochemists/enzymologists interested in gaining detailed insight into protein-ligand / enzyme-substrate complexes.

 

Requirements: Basic knowledge of protein (crystal) structures, ideally some familiarity with PyMOL.

 

Description:

Enlighten is a new (free and open) plugin to PyMOL with integrated protocols for automated simulation of a protein (enzyme) with a ligand bound (e.g. substrate or inhibitor). All software that it uses is available without charges or subscriptions.

In this tutorial workshop, aimed specifically at people not familiar with biomolecular simulation, we will show how the plugin can be used to perform simulation of protein-ligand (enzyme-substrate) easily and on standard computers. This should thus provide a new way to gain insights that go beyond static (docked or crystallographic complex) structures, including for enzyme function, design and inhibition.

The tutorial will be run on Linux computers, but will not require any experience with Linux. (The current tools are available for Linux and Mac OSX, with a future aim to make them available for Windows as well.)

This tutorial workshop will also be an opportunity to provide feedback for the future development of these tools.

 

See also the current development of the tools:

https://github.com/marcvanderkamp/enlighten

 

Accommodation

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

 

Contact

For queries related to this days workshop contact:

This email address is being protected from spambots. You need JavaScript enabled to view it.

 

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.