Source:Protein structure prediction (3rd Edition), Methods in Molecular Biology, Daisuke Kihara, Ed., 1137:235-250, 2014
Coarse-grained (CG) modeling is a well-acknowledged simulation approach for getting insight into long timescale protein folding events at reasonable computational cost. Depending on the design of a CG model, the simulation protocols vary from highly case-specific – requiring user-defined assumptions about the folding scenario, to more sophisticated blind prediction methods for which only a protein sequence is required. Here we describe the framework protocol for the simulations of long-term dynamics of globular proteins, with the use of the CABS CG protein model and sequence data. The simulations can start from a random or selected (e.g. native) structure. The described protocol has been validated using experimental data for protein folding model systems – the prediction results agreed well with the experimental results.