Computational Modelling Group

Structural biology

Structural biology is concerned with the physical and mechanical properties of biological molecules, including proteins, nucleotides, lipids, drugs and other small molecules. Topics include computational techniques for interpreting experimental data (e.g. NMR and X-Ray crystallography) as well as methods for predicting structure and function in the absence of experimental data (e.g. homology modelling and molecular dynamics).

Image courtesy: Phil Williamson

For queries about this topic, contact Philip Williamson.

View the calendar of events relating to this topic.

Projects

Centre for Doctoral Training in Next Generation Computational Modelling

Hans Fangohr, Ian Hawke, Peter Horak (Investigators), Susanne Ufermann Fangohr, Ryan Pepper, Hossam Ragheb, Emanuele Zappia, Ashley Setter, David Lusher, Alvaro Perez-Diaz, Kieran Selvon, Thorsten Wittemeier, Mihails Milehins, Stephen Gow, Ioannis Begleris, Jonathon Waters, James Harrison, Joshua Greenhalgh, Rory Brown, Robert Entwistle, Paul Chambers, Jan Kamenik, Craig Rafter

The £10million Centre for Doctoral Training was launched in November 2013 and is jointly funded by EPSRC, the University of Southampton, and its partners.

The NGCM brings together world-class simulation modelling research activities from across the University of Southampton and hosts a 4-year doctoral training programme that is the first of its kind in the UK.

Control and Prediction of the Organic Solid State

Richard Boardman

This project aims to produce a computer technology for the prediction of the crystal structure(s) of an organic molecule, that could be used even prior to the synthesis of the compound.

Such a computational study could be done relatively quickly to predict the dangers and opportunities of the solid phases of a molecule under development. Our project will develop the methods of experimental screening for polymorphs and their characterisation, and hence the combination will provide a major new technology for aiding industrial formulation.

How far can we stretch the MARTINI?

Syma Khalid (Investigator), Ric Gillams

To date, coarse-grained lipid models have generally been parameterised to ensure the correct prediction of structural properties of membranes, such as the area per lipid and the bilayer thickness. The work described here explores the extent to which coarse-grained models are able to predict correctly bulk properties of lipids (phase behaviour) as well as the mechanical properties, such as lateral pressure profiles and stored elastic stress in bilayers. Such an evaluation is crucial for understanding the predictive capabilities of coarse-grained models.

Immunotherapy Research: Modelling MHC Class I Complex Assembly

Timothy Elliott, Jorn Werner (Investigators), Alistair Bailey

This project uses mathematical modelling and simulation to investigate mechanisms by which our cells process and present biological information that is used by our immune system to distinguish between healthy and diseased cells.

Integrated in silico prediction of protein-protein interaction motifs

Richard Edwards (Investigator), Nicolas Palopoli, Kieren Lythgow

Many vital protein-protein interactions are mediated by Short Linear Motifs (SLiMs) which are short proteins typically 5-15 amino acids long containing only a few positions crucial to function. This project integrates a number of leading computational techniques to predict novel SLiMs and add crucial detail to protein-protein interaction networks.

Multiscale modelling of biological membranes

Jonathan Essex (Investigator), Mario Orsi

Biological membranes are complex and fascinating systems, characterised by proteins floating in a sea of lipids. Biomembranes, besides being the fundamental structures employed by nature to encapsulate cells, play crucial roles in many phenomena indispensable for life, such as growth, energy storage, and in general information transduction via neural activity. In this project, we develop and apply multiscale computational models to simulate biological membranes and obtain molecular-level insights into fundamental structures and phenomena.

The application and critical assessment of protein-ligand binding affinities

Jonathan Essex (Investigator), Ioannis Haldoupis

A method that can accurately predict the binding affinity of small molecules to a protein target would be imperative to pharmaceutical development due to the time and resources that could be saved. A head-to-head comparison of such methodology, ranging from approximate methods to more rigorous methods, is performed in order to assess their accuracy and utility across a range of targets.

The autotransporter β domain: insights into structure and function through multi scale molecular dynamics simulations

Syma Khalid (Investigator), Daniel Holdbrook, Thomas Piggot

We are performing a series of molecular dynamics simulations involving all autotransporters with known structure. We aim to identify key structural and dynamic properties in this family of proteins.

Using Molecular Dynamics to Understand the Antibacterial Mechanisms of Daptomycin & Chlorhexidine to Target the Bacterial Membrane

This project aims to use molecular dynamics techniques to understand how antimicrobial peptides, daptomycin and chlorhexidine, disrupt both gram positive and negative cell membranes on an atomic level.

Using Molecular Dynamics to Understand the Antibacterial Mechanisms of Daptomycin & Chlorhexidine to Target the Bacterial Membrane

This project aims to use molecular dynamics techniques to understand how antimicrobial peptides, daptomycin and chlorhexidine, disrupt both gram positive and negative cell membranes on an atomic level.

Using Molecular Dynamics to Understand the Antibacterial Mechanisms of Daptomycin & Chlorhexidine to Target the Bacterial Membrane

Syma Khalid (Investigator), Eilish McBurnie

This project aims to use molecular dynamics techniques to understand how antimicrobial peptides, daptomycin and chlorhexidine, disrupt both gram positive and negative cell membranes on an atomic level.

People

Andrew Collins
Professor, Medicine (FM)
Timothy Elliott
Professor, Medicine (FM)
Jonathan Essex
Professor, Chemistry (FNES)
Hans Fangohr
Professor, Engineering Sciences (FEE)
Anthony Postle
Professor, Medicine (FM)
Peter Horak
Reader, Optoelectronics Research Centre
Tiina Roose
Reader, Engineering Sciences (FEE)
Jorn Werner
Reader, Biological Sciences (FNES)
Ian Hawke
Lecturer, Mathematics (FSHS)
Syma Khalid
Principal Research Fellow, Chemistry (FNES)
Richard Boardman
Senior Research Fellow, Engineering Sciences (FEE)
Philip Williamson
Senior Research Fellow, Biological Sciences (FNES)
Alistair Bailey
Research Fellow, Medicine (FM)
Gaia Andreoletti
Postgraduate Research Student, Medicine (FM)
Ioannis Begleris
Postgraduate Research Student, Engineering Sciences (FEE)
Louise Bolton
Postgraduate Research Student, Medicine (FM)
Rory Brown
Postgraduate Research Student, Civil Engineering & the Environment (FEE)
Paul Chambers
Postgraduate Research Student, Engineering Sciences (FEE)
Paul Cross
Postgraduate Research Student, Engineering Sciences (FEE)
Caroline Duignan
Postgraduate Research Student, Biological Sciences (FNES)
Robert Entwistle
Postgraduate Research Student, Engineering Sciences (FEE)
Ric Gillams
Postgraduate Research Student, Chemistry (FNES)
Stephen Gow
Postgraduate Research Student, Engineering Sciences (FEE)
Joshua Greenhalgh
Postgraduate Research Student, Engineering Sciences (FEE)
Ioannis Haldoupis
Postgraduate Research Student, Chemistry (FNES)
James Harrison
Postgraduate Research Student, Engineering Sciences (FEE)
William Hurndall
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Jan Kamenik
Postgraduate Research Student, Engineering Sciences (FEE)
David Lusher
Postgraduate Research Student, Engineering Sciences (FEE)
Alvaro Perez-Diaz
Postgraduate Research Student, Engineering Sciences (FEE)
Can Pervane
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Craig Rafter
Postgraduate Research Student, Engineering Sciences (FEE)
Hossam Ragheb
Postgraduate Research Student, Engineering Sciences (FEE)
Kieran Selvon
Postgraduate Research Student, Engineering Sciences (FEE)
Ashley Setter
Postgraduate Research Student, Engineering Sciences (FEE)
Jonathon Waters
Postgraduate Research Student, Engineering Sciences (FEE)
Thorsten Wittemeier
Postgraduate Research Student, Engineering Sciences (FEE)
Emanuele Zappia
Postgraduate Research Student, Engineering Sciences (FEE)
Matthew Higgins
Undergraduate Research Student, Biological Sciences (FNES)
Elena Vataga
Technical Staff, iSolutions
Petrina Butler
Administrative Staff, Research and Innovation Services
Susanne Ufermann Fangohr
Administrative Staff, Civil Engineering & the Environment (FEE)
Richard Edwards
Alumnus, University of New South Wales, Australia
Kieren Lythgow
Alumnus, Health Protection Agency
Mihails Milehins
Alumnus, University of Southampton
Nicolas Palopoli
Alumnus, Biological Sciences (FNES)
Mario Orsi
External Member, Queen Mary University of London
Daniel Holdbrook
None, None
Eilish McBurnie
None, None
Thomas Piggot
None, None