CCPBioSim

CCP-BioSim is the Collaborative Computational Project for Biomolecular Simulation. It was set up in 2011 with support from EPSRC to support and promote biomolecular simulation in the UK. Biomolecular simulation is increasingly contributing to biology and important in drug design.CCP-BioSim also aims to identify methodological and computational challenges in this growing field. CCP-BioSim organizes training workshops and provides a framework for networking and collaboration.CCP-BioSim develops and delivers training and tools to lower the barrier to non-experts becoming proficient and productive users of biomolecular simulation techniques. We also work to develop and apply advanced methods, particularly develop practical integrated approaches to multiscale simulations for biomolecular systems.

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Check out details of the 4TH CCPBIOSIM/CCP5 CONFERENCE ON MULTISCALE MODELLING OF CONDENSED PHASE AND BIOLOGICAL SYSTEMS

4th CCPBioSim/CCP5 Conference on Multiscale Modelling of Condensed Phase and Biological Systems | CCP5 Computer Simulations of Condensed Pha

http://www.ccp5.ac.uk/node/350

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Hot new research from CCPBioSim members

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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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Computational Chemistry Gordon Conference

https://www.grc.org/programs.aspx?id=11141

Theory and Simulation Across Scales in Molecular Science Dates

July 24-29, 2016 Location

PGA Catalunya Business and Convention Centre Girona, Spain Site Information Organizers

Chair: Adrian J. Mulholland

Vice Chair: Angela Wilson

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Showcase: QM/MM calculations of the RNase H two-metal ion catalytic reaction. The movie shows the basic steps of a simulation setup as the water molecules and KCl are added to the simulations system. The two Mg ions are also highlighted in positions A and B together with the scissile phosphate bond. 

Rosta, Yang, Hummer,  J. Am. Chem. Soc., 2014 & 2011

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Dynamics of the MDM2 protein lid region (green) in absence of any ligand.

MDM2 is a protein implicated in the progression of many forms of cancer. A possible strategy for developing new anti-cancer agents is to find small-molecules that can bind to the protein MDM2. The process is easier if the atomic structure of MDM2 is known. However, only the structure of the MDM2 core region (blue) is known from experiments. Simulations have been used here to determine the structure of a missing element, the lid region (green). The simulations show that the lid region is very dynamic, which explains also why it is difficult to determine the structure of this region with experiments.

Bueren-Calabuig & Michel (unpublished)

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Dynamics of the MDM2 protein lid region (green) in presence of a Bzd inhibitor.

MDM2 is a protein implicated in the progression of many forms of cancer. A possible strategy for developing new anti-cancer agents is to find small-molecules that can bind to the protein MDM2. The process is easier if the atomic structure of MDM2 is known. However, only the structure of the MDM2 core region (blue) is known from experiments. Simulations have been used here to determine the structure of a missing element, the lid region (green). The simulations show that the lid region is very dynamic, which explains also why it is difficult to determine the structure of this region with experiments.

Here the structure of the lid region has been solved in the presence of a known MDM2 ligand (called Bzd). By comparison with the video above, it can be seen that the Bzd ligand strongly influences the dynamics of the MDM2 lid region. The details of the interactions of the Bzd molecule with the lid region offer precious insights that can help drug designers develop better MDM2 ligands, that ultimately could become anti-cancer agents.

Bueren-Calabuig & Michel (unpublished)

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Coarse-grain MD simulation of phospholipid self-assembly into a bilayer around the E.coli outer membrane protein, OmpA.

Bond & Sansom, 2006, Journal of the American Chemical Society

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Showcase: the antimicrobial peptide, melittin (from honey bee toxin) interacting with PC phosphlipids.

Khalid & Berglund (unpublished)

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Showcase: movies from MD simulations

Coarse grain simulation of a lipid vesicle containing outer membrane proteins of E.coli

Holdbrook & Khalid (unpublished)

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Showcase: movies from MD simulations

Insertion of ssDNA into a model of the alpha hemolysin barrel, under an applied electric field. 

Bond, Guy, Heron, Bayley & Khalid, Biochemistry, 2011

These work was funded by Oxford Nanopore Technologies.

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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.

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CHECK OUT DETAILS OF OUR LATEST CONFERENCE

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Computational enzymology is a rapidly growing area, with modelling increasingly being recognised as essential for understanding these fascinating biological catalysts.

Click on the title text to read more

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A one-day workshop to be held in Cambridge on March 20th 2013.

ideal for beginners in Molecular Dynamics simulations of biological molecules.

Click on the title text to go the event webpage.

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Deadline for registering for our annual conference fast approaching

Please see the link below for details:

http://www.ccpbiosim.ac.uk/?q=annualconfs/conf2013