How to Set Up a Protein Simulation- free workshop!
A one-day workshop to be held in Cambridge on March 20th 2013.
ideal for beginners in Molecular Dynamics simulations of biological molecules.
Systems & Synthetic Biology Modelling Group
Welcome to the official blog of the Systems & Synthetic Biology Modelling Group, headed by Dr Syma Khalid, in Chemistry at the University of Southampton, UK.
We are a computational chemistry/biochemistry group with a core research interest in events that occur in, and around biological membranes.
Please see: http://www.personal.soton.ac.uk/sk2x07/index.php for our research pages.
This blog will provide the latest information regarding our research activities, some of our own publications, papers from other groups that have interested us and recent research areas that have caught our imagination. If this sounds interesting, then please do follow us!
Contact S.Khalid@soton for any thoughts or comments on this blog.
February182013
December232012
Funded PhD studentships available
Please contact S.Khalid@soton.ac.uk for further details.
7PM
Andrew’s celebration cake. Complete with beta barrel protein constructed from curly wurly bars and ssDNA constructed from jelly snakes
December222012
Cut-away through a vesicle containing E.coli outer membrane proteins. This coarse-grained, solvated system is composed of over 1 million particles. It has been studied by MD simulations using the GROMACS simulation package on the IridisIII HPC resource at the University of Southampton
8AM
Andrew Guy successfully defends his PhD thesis!
Great start to the Christmas holidays for the group.
November132012
ssDNA in a simplified nanopore based on the alpha hemolysin barrel.
Biophys J. 2012 Sep 5;103(5):1028-36.
Single-Stranded DNA within Nanopores:
Conformational Dynamics and Implications for sequencing; a Molecular Dynamics Simulation Study.
October282012
Andrew Guy submits his thesis- first one from the Khalid group!
October112012
CCPBioSim workshop: Free energy methods for modelling of protein-ligand interactions
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-stage career researchers.
Reference
“Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations”, Michel, J. ; Essex, J. W. J. Comput. Aided Mol. Des., 24 (8), 639 -658 2010 http://dx.doi.org/10.1007/s10822-010-9363-3
For additional details please see
September192012
Moving into our newly refurbished lab.
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