Molecular Simulations and Biomembranes (eBook)

Philip Biggin is a Senior Research Associate in the Department of Biochemistry at the University of Oxford. His research interests lie in receptor-ligand interactions, comparative dynamics of proteins and bioinformatics of ligand-gated ion channels. He is the author of over 30 peer-reviewed papers and he sits on the Oxford Supercomputing Centre management committee. He is currently a consultant to BioMedCentral on the development and implementation of cysloopDB, a database that stores all of the physiological and pharmacological data for the cys-loop family of ligand-gated ion channels. He is a member of the Royal Society of Chemistry, the British Biophysical Society, the Biochemical Society, the US Biophysical Society, and the Molecular Graphics and Modelling Society. Mark Sansom is a Professor in the Department of Biochemistry at the University of Oxford, and Director of the Structural Bioinformatics and Computational Biochemistry Unit (http://sbcb.bioch.ox.ac.uk). He has worked on modelling and simulations of membrane proteins for over 15 years. He heads a research group of about 25 people working on topics ranging from the dynamics of water in nanopores to large scale MD simulations of bacterial membranes. This is currently funded by BBSRC, the Wellcome Trust, the EPSRC (as part of the bionanotechnology IRC), and MRC. He is the author of about 275 papers and reviews. He has an interest in HPC and in GRID computing for biomolecular simulation applications, and heads the BioSimGrid (www.biosimgrid.org) and IntBioSim (www.intbiosim.org) projects, in addition to a project (funded by BBSRC and IBM/HPCx) to develop a virtual outer membrane. He is a member of the High End Computing Strategy Committee, and the HPC Trends and Opportunities Panel (representing BBSRC interests on both), and chairs the Hector Science Board. He is an editorial board member for several journals, including Biophysical Journal, Physical Biology, Protein Engineering, Selection & Design, and Molecular Membrane Biology. He is also a Fellow of the Institute of Physics, and a member of the Biochemical Society, the US Biophysical Society, and the Physiological Society.

Introduction & overview Methodologies and parameters for membrane simulations Atomistic simulations of lipid bilayers (simple and complex) Coarse-grained simulations of lipids bilayers Bilayers and small molecule (drug) permeability Peptides & proteins - insertion, folding Bionanotechnology and membrane simulations Potassium channels Ligand-gated ion channels G-Protein couple receptors Bacterial outer membrane proteins Transport proteins Multi-scale simulations for large systems