#ccpbiosim

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Scientists from the Universities of Bristol and Parma, Italy, have used molecular simulations to understand resistance to osimertinib - an anticancer drug used to treat types of lung cancer.

CCPBioSim members using simulations to better understand the effects of anticancer drugs 

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CCPBioSim is the Collaborative Computational Project for Biomolecular Simulation, funded by the EPSRC.

Our latest training week is coming up! Check out the link & sign up.

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2013 Nobel Prize in Chemistry goes to Multiscale Simulation!

The press release from: http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/press.html 

The computer – your Virgil in the world of atoms

Chemists used to create models of molecules using plastic balls and sticks. Today, the modelling is carried out in computers. In the 1970s, Martin Karplus, Michael Levitt and Arieh Warshel laid the foundation for the powerful programs that are used to understand and predict chemical processes. Computer models mirroring real life have become crucial for most advances made in chemistry today.

Chemical reactions occur at lightning speed. In a fraction of a millisecond, electrons jump from one atomic to the other. Classical chemistry has a hard time keeping up; it is virtually impossible to experimentally map every little step in a chemical process. Aided by the methods now awarded with the Nobel Prize in Chemistry, scientists let computers unveil chemical processes, such as a catalyst’s purification of exhaust fumes or the photo­synthesis in green leaves.

The work of Karplus, Levitt and Warshel is ground-breaking in that they managed to make Newton’s classical physics work side-by-side with the fundamentally different quantum physics. Previously, chemists had to choose to use either or. The strength of classical physics was that calculations were simple and could be used to model really large molecules. Its weakness, it offered no way to simulate chemical reactions. For that purpose, chemists instead had to use quantum physics. But such calculations required enormous computing power and could therefore only be carried out for small molecules.

This year’s Nobel Laureates in chemistry took the best from both worlds and devised methods that use both classical and quantum physics. For instance, in simulations of how a drug couples to its target protein in the body, the computer performs quantum theoretical calculations on those atoms in the target protein that interact with the drug. The rest of the large protein is simulated using less demanding classical physics.

Today the computer is just as important a tool for chemists as the test tube. Simulations are so realistic that they predict the outcome of traditional experiments.

[jmichel80-blog]

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

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

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1st CCP-BioSim Conference: Frontiers of Biomolecular Simulation

The  first conference organized by CCP-BioSim, the Collaborative Computational Project for Biomolecular Simulation was held at the Royal Agricultural College, Cirencester in June 2012. The conference highlighted cutting edge work in biomolecular simulation, with a  particular focus on connecting simulations with experiments.

Speakers were:

Robert Best (University of Cambridge)

Phil Biggin (University of Oxford)

Julien Michel (University of Edinburgh)

Luca Monticelli (INSERM Paris)

This meeting was a satellite meeting of Computational Molecular Science. The morning session of CMS on Wednesday June 27th will also have a biomolecular simulation focus.

[ccpbiosim]

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

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 aimed at postgraduate students and early-stage career researchers. The CHARMM program will be used.

Reference: A practical guide to modelling enzyme-catalysed reactions Lonsdale R, Harvey JN, Mulholland AJ Chem. Soc. Rev. (2012), vol. 41, pp. 3025-3038 http://dx.doi.org/10.1039/C2CS15297E

For additional details please see: https://eventbooking.stfc.ac.uk/news-events/ccpbiosim-training-workshop-qmmm-methods-for-modelling-enzyme-catalysed-reactions

[ccpbiosim]

CCPBioSim workshop: How to set up a protein simulation

The first CCPBioSim training workshop was held in Cambridge in April 2012

The workshop tutors were Peter Bond (Cambridge) and Syma Khalid (Southampton)

More details to appear here soon.

[symakhalidresearchgroup]

CCPBioSim workshop: How To Set Up a Protein Simulation

This free, one day workshop held in Cambridge was a successful first event for the EPSRC-funded CCPBioSim initiative. The 16 conference attendees had a busy day of learning theoretical aspects of running molecular dynamics simulations of soluble proteins, as well as hands-on practical work. The workshop was run by Dr Syma Khalid (Southampton) and Dr Peter Bond (Cambridge)