Homology modeling and coarse-grained molecular dynamics studies

In this lecture difficulties inherited from protein structure prediction techniques will be discussed for ligand gated ion channels along with enhanced molecular dynamics simulations (MD) and normal mode analysis.The accuracy of comparative models derived from homologous proteins in the low sequence similarity range is limited substantially by inaccuracies in the alignment. In spite of recent advances in profile-profile, profile-sequence, and other alignment methods, the accuracy of the alignments remains a primary factor in the accuracy of the final model. In this lecture various different alternative techniques based on iterative approaches of model building and model assesment will be discussed along with standard protein structure modeling techniques. Additionally, molecular dynamics of NMDA type tetrameric and nicotinic acetyl choline type pentameric ion channel proteins will be discussed to illustrate the current status of all-atom molecular dynamics studies.