E-mail: Mark.Sansom{at}bioch.ox.ac.uk

[ About IntBioSim | Centres for the four levels of Simulation | Computer Scientists | Presentations | Publications | Links for websites of the Principal Investigators | Documentation]

The overall aim of this project is to explore and establish an integrated approach to computational systems biology spanning from the chemical to the subcellular level of simulations. Biomolecular simulations play a key role in enabling us to study and understand biological processes at a microscopic level, not always accessible to experiment. Thus simulations are essential for interpretation and extension of experimental information, and are becoming increasingly important as methods and computer technology advance. Biomolecular simulations are also a key element of a genuine predictive biology, enabling us to employ the results of structural biology in a non-reductionist fashion. However, no single method can achieve all the levels of detail needed. Hence, we wish to integrate simulations ranging in level from the mechanistic (i.e. bond breaking and making) through ligand-protein interactions and conformational changes to ligand diffusion in a membrane. In the course of these studies we will exploit the biological usefulness of this approach, and will develop the use of HPC in multi-level biomolecular simulations. This will have a strong multi-disciplinary element and will bring to biological modelling both e-Science and simulation techniques from the physical and computational sciences.

Schematic representation of the levels of simulation in the IntBiosim project. The figure on the left displays the overview of simulation approaches in the IntBioSim project. The figure on the right further describes the interaction between the four levels of simulation.

Centres for the four levels of Simulation

1) M1. Physical location: London (UCL)

Prof. Coveney's group have considerable experience of dissapative particle dynamics (DPD), which will be applied to monotopic proteins (the biological system of interest to the IntBiosim project). Postdoc in charge: Dr. Shunzhou Wan

2) M2. Physical location: Oxford Biochemistry

Prof. Sansom's group have extensive expertise in molecular dynamics (MD) simulations and are now developing coarse grain MD approaches to membrane bound monotopic proteins. Postdoc in charge: Dr. Kia Balali-Mood

3) M3. Physical location: Southampton

Dr. Essex's group have considerable experience of drug docking studies. A range of docking algorithms will be used to quantify the fit of a ligand to the binding site of monotopic proteins.Postdoc in charge: Dr. Frank Beierlein

4) M4. Physical location: Bristol

Dr. Mulholland's group have substansial expertise in quantum mechanical/molecular mechnanics (QM/MM). This is a hybrid approach, and now that data has been generated from the lower levels of simulation, the QM/MM approach will be employed. Postdoc in charge: Dr. Christo Christov

Computer Scientists

IntBioSim is a collaborative project and without the considerable expertise of Computational Scientists at Manchester and the Comlab (Oxford) it would not have been possible. Principal Investigators are Profs. David Gavaghan (Oxford) and John Gurd (Manchester) as well as Dr.Steve McKeever (Oxford). Two highly talented Research Fellows based in Manchester (School of Computer Science) are Graham Riley and Rupert Ford.

Presentations