Abstract
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.
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Acknowledgments
The authors acknowledge support from a TEAM project (TEAM/2011-7/6) co-financed by the EU European Regional Development Fund operated within the Innovative Economy Operational Program and from Polish National Science Center (Grant No. NN301071140) and from Polish Ministry of Science and Higher Education (Grant No. IP2011 024371).
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Jamroz, M., Kolinski, A., Kmiecik, S. (2014). Protocols for Efficient Simulations of Long-Time Protein Dynamics Using Coarse-Grained CABS Model. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 1137. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0366-5_16
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DOI: https://doi.org/10.1007/978-1-4939-0366-5_16
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