Coarse-grained (CG) modeling is a well-acknowledged simulation approach for getting insight into long-time scale 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 a 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.
CITATION STYLE
Jamroz, M., Kolinski, A., & Kmiecik, S. (2014). Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model. Methods in Molecular Biology, 1137, 235–250. https://doi.org/10.1007/978-1-4939-0366-5_16
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