Approaches to ab initio folding Full Md with explicit solvation( e.g. IBM Blue Gene) VERY expensive May not work Reduced complexity models No side chains(sometimes no main chain atoms either!) Reduced degrees of freedom On-or off-lattice Generally have a solvation-based score and a knowledge based residue-residue interaction term Sometimes used as first step to prune the enormous conformational space then resolution is increased for later fine-tuningApproaches to ab initio folding • Full MD with explicit solvation (e.g. IBM Blue Gene) – VERY expensive – May not work • Reduced complexity models – No side chains (sometimes no main chain atoms either!) – Reduced degrees of freedom – On- or off-lattice – Generally have a solvation-based score and a knowledge￾based residue-residue interaction term – Sometimes used as first step to prune the enormous conformational space, then resolution is increased for later fine-tuning