Molecular Dynamics at VLSCI

Since August 2010, when Jason Roberts demonstrated what great virus models he could make with the capacity now available to him, Victoria's molecular dynamics (MD) researchers have been making full use of VLSCI's systems.  The skills of our resident expert, Dr Michael Kuiper, have been requested across a range of projects, where he collaborates with many research teams across Victoria to improve their access MD tools and techniques.

In response to the growing demand in this field, VLSCI's Life Sciences Computation Centre (LSCC) has established an MD 'theme'. Based at the La Trobe Institute for Molecular Science (LIMS), Theme Leader, A/Prof. Brian Smith (Faculty of Science, Technology and Engineering), will work with newly appointed Dr Michael Thomas to strategically focus skills and resources on research projects using or wanting to use, MD. Dr Thomas has been working as a Postdoctoral Research Fellow, Research School of Biology at ANU. He is interested in computational modelling of biological molecules, particularly in the transport properties of channels and transporters. He is keen to adapt the knowledge gained from the study of these "marvellous" proteins for use in nanotechnology, as well further study into the interface between biology and nanotechnology. Dr Kuiper will continue to work in Carlton from Monday to Thursday, and now be at LIMS on Fridays.

ACTIVITIES TO DATE:

New Toolkit

Over 2012, VLSCI established a much-requested computational biology toolkit, focussing initially on genomics and MD. Link to it straight from the VLSCI home page. More tutorials and materials are being developed and added by LSCC experts throughout 2013/14.

Supported Projects

Currently, the LSCC has a range of supported projects in addition to those project teams using its subscription service. If you are wanting support for your MD work from the LSCC, details are here. Some of the MD projects currently receiving LSCC support are:
• Modelling pore-forming toxins, Prof. Michael Parker, St Vincent's Institute
• Development of Molecular Dynamics Drug Docking, Prof. Matthew Wilce, Monash University
• Molecular Modelling of Novel Enterovirus Proteins Associated With Acute Flaccid Paralysis, Victorian Infectious Diseases Laboratory
• Molecular modelling of plasma albumin for development of brain drug delivery, Prof. Norman Saunders, University of Melbourne


Workshops


VLSCI runs regular free workshops with interactive sessions and hands-on exercises and lots of opportunities for you to discuss your research needs:
• Introduction to high performance computing at VLSCI: 3 hours (Dr Andrew Isaac)
• Introduction to molecular modelling and visualisation in the life sciences: 3 hours (Dr Michael Kuiper)
• Intermediate molecular modelling and visualisation for life sciences research: 3 hours (Dr Michael Kuiper)


Work experience student, Ben Harper, Camberwell High School, has recently given up the first week of his holidays to continue developing his digitally printed molecular models, under close supervision by Dr Kuiper and with assistance from Dr Bernard Meade, ITS, University of Melbourne. It is terrific to see such enthusiasm from Ben and we hope we have inspired a future computational biologist. VLSCI has also provided intensive training of several postgraduate students in MD techniques during summer internships, and continues to support undergraduate students undertaking MD projects as part of the Undergraduate Research Opportunities Program.

 

FUTURE MD EVENTS:

Friday 16 August 2013, 3-4.30pm with refreshments from 4.30-6 - VLSCI Boardroom


Researchers and students are eligible to apply for VLSCI conference and travel grants at any time. One requirement of these grants is that recipients share their experience with our community. We have set aside Friday 16 August for presentations focussed on MD events. Please register your interest in attending with Christina Hall.

24-27 November 2013, Australian Society for Biophysics, 2013 meeting


VLSCI is pleased to be sponsoring this event. Organisers include active VLSCI users, Dr Andrew Hung and A/Prof. Toby Allen, VC Senior Research Fellow, School of Applied Science & Health Innovations Research Institute, RMIT University. A/Prof. Allen has moved back to Australia after 10 years in the US, where he worked at UC Davis.

February 2014


In 2011, VLSCI sponsored the annual M4 conference in Melbourne. The next conference is to be in February 2014, coinciding with the Lorne Protein conference, also sponsored by VLSCI. The Lorne conference program has a computational biology stream and will feature work currently running on our systems. M4 offers a chance for the MD community to get together and share their research.

Dates to note:  M4 conference date - TBC;  39th Lorne Protein Structure & Function Conference, 9-13 February 2014.

All upcoming workshops, meetings and opportunities are announced via our website, e-News, twitter and Linked In groups. Go to the VLSCI homepage to sign up for any of these services.
Researchers and students may also be eligible for support to attend conferences through VLSCI's travel and conference grant program.Please send any enquiries to A/Prof. Brian Smith or Head, LSCC, A/Prof. Andrew Lonie.

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