Systems & Synthetic Biology Modelling Group

How to Set Up a Protein Simulation- free workshop!

Mon, 18 Feb 2013 07:51:03 -0500

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.

Funded PhD studentships available

Sun, 23 Dec 2012 20:20:40 -0500

Please contact S.Khalid@soton.ac.uk for further details.

sykhalid: Andrew’s celebration cake. Complete with beta barrel...

Sun, 23 Dec 2012 19:06:29 -0500

sykhalid:

Andrew’s celebration cake. Complete with beta barrel protein constructed from curly wurly bars and ssDNA constructed from jelly snakes

Cut-away through a vesicle containing E.coli outer membrane...

Sat, 22 Dec 2012 09:03:30 -0500

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

Andrew Guy successfully defends his PhD thesis!

Sat, 22 Dec 2012 08:58:47 -0500

Great start to the Christmas holidays for the group.

ssDNA in a simplified nanopore based on the alpha hemolysin...

Tue, 13 Nov 2012 16:40:00 -0500

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.

Guy AT, Piggot TJ, Khalid S.

ccpbiosim: CCPBioSim Annual Conference: 2013

Tue, 13 Nov 2012 16:37:36 -0500

ccpbiosim:

CCPBioSim Annual Conference: 2013

Andrew Guy submits his thesis- first one from the Khalid group!

Sun, 28 Oct 2012 16:09:05 -0400

Andrew Guy submits his thesis- first one from the Khalid group!

CCPBioSim workshop: Free energy methods for modelling of protein-ligand interactions

Thu, 11 Oct 2012 14:44:10 -0400

CCPBioSim workshop: Free energy methods for modelling of protein-ligand interactions :

ccpbiosim:

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

http://ccpbiosim.chm.bris.ac.uk/?q=workshops/1stFreeEnergy

Moving into our newly refurbished lab.

Wed, 19 Sep 2012 05:52:00 -0400

Moving into our newly refurbished lab.

FecA protein from the outer membrane of E.coli, embedded in an...

Thu, 06 Sep 2012 20:14:17 -0400

FecA protein from the outer membrane of E.coli, embedded in an asymmetric model of the outer membrane environment. Soon to be published in Piggot, Holdbrook and Khalid, BBA Biomembranes, 2012.

Refurbishment of our lab begins

Sat, 25 Aug 2012 16:36:05 -0400

The group will move into our new home in time for the start of the new term when we will be joined by new graduate and undergraduate students.
Photos to come.

University of Southampton supercomputer to help give unprecedented processing power to business and academics

Thu, 12 Jul 2012 05:50:00 -0400

The UK’s most powerful GPU-based supercomputer, “Emerald”, has entered into service today, alongside the University of Southampton’s own supercomputer “Iridis 3”. The combination of these two High Performance Computing systems will give businesses and academics unprecedented access to their super-fast processing capability.

Both supercomputers were unveiled at the Science and Technology Facilities Council’s Rutherford Appleton Laboratory, which hosts and operates Emerald, a GPU system utilising NVIDIA’s Tesla accelerator technology. Iridis 3, hosted by the University of Southampton, was launched in 2010 when it was ranked position 74 in the top 500 supercomputers worldwide. It has a 12,000 core Intel Westmere based general architecture/x86 based system.

Both supercomputers have been funded by a £3.7 million grant from the Engineering and Physical Sciences Research Council (EPSRC), to the e-Infrastructure South Consortium which comprises four of the UK’s leading universities – Southampton, Bristol, Oxford and University College London, as part of a £145 million Government investment in e-infrastructure.

To read some of the media coverage surrounding the IridisIII upgrade and launch of Emerald, follow the links below:

http://www.newelectronics.co.uk/electronics-news/uks-most-powerful-gpu-based-supercomputer-enters-service-today/43437/

http://www.scienceomega.com/article/460/towards-sound-e-infrastructure-supercomputers-unveiled

CCPBioSim: CCPBioSim workshop: QM/MM Methods for Modelling Enzyme-catalyzed Reactions

Thu, 12 Jul 2012 05:11:35 -0400

CCPBioSim: CCPBioSim workshop: QM/MM Methods for Modelling Enzyme-catalyzed Reactions:

ccpbiosim:

The second CCPBioSim training workshop will take place in Bristol on Tuesday, 17th July 2012

This CCPBioSim training workshop will introduce non-specialists to the use of combined quantum mechanics/molecular mechanics (QM/MM) methods for modelling enzyme-catalysed reaction mechanisms. It is…

This movie shows the top view of a melittin (venom from honey...

Wed, 11 Jul 2012 08:47:00 -0400

This movie shows the top view of a melittin (venom from honey bees) tetramer embedded in a POPE lipid bilayer.

CECAM meeting on Free Energy Calculations

Sun, 10 Jun 2012 10:34:00 -0400

Free energy calculations: From theory to applications

June 4, 2012 to June 8, 2012

Location : Ecole des Ponts, Champs-sur-Marne, France.

http://www.cecam.org/workshop-695.html

This workshop featured talks from a combination of established high profile speakers as well as younger researchers.

A number of themes arose from this workshop, the overarching one being that there is still no ‘best way’ to calculate free energies from molecular simulations. Workshops like this, are essential in facilitating discussion and disseminating the latest findings. Given that new methods are being developed and refined, disseminating the latest progress in a timely fashion is of utmost importance.

A very useful resource from Michael Shirts’ lab:

http://www.alchemistry.org/wiki/index.php?title=Main_Page

In Pisa for a CECAM meeting: DNA sequencing and detection with...

Sun, 10 Jun 2012 10:26:00 -0400

In Pisa for a CECAM meeting:

DNA sequencing and detection with nanoprobes
Scuola Normale Superiore, Pisa, Italy
June 11, 2012 to June 13, 2012

http://www.cecam.org/workshop-822.html

A beautiful city in which to hold conferences!

Prestigious PhD studentships available

Thu, 24 May 2012 18:17:00 -0400

4-year studentships are available to work in Dr Syma Khalid’s group the Institute for Complex Systems Simulation Doctoral Training Centre at the University of Southampton.

For details see:

http://www.icss.soton.ac.uk/programme/index.html

Please send informa enquiries to Dr Syma Khalid via email : S.Khalid@soton.ac.uk

FhuA; a TonB-dependent transporter from the outer membranes of...

Sat, 19 May 2012 10:31:00 -0400

FhuA; a TonB-dependent transporter from the outer membranes of E.coli.
Rendered with VMD

Computational Molecular Science 2012

Sat, 19 May 2012 10:24:26 -0400

followed by the first CCPBioSim satellite conference:

http://www.chm.bris.ac.uk/cms/