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Protocols for Efficient Simulations of Long-Time Protein Dynamics Using Coarse-Grained CABS Model

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1137)

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.

Keywords

Folding pathway Folding mechanism Protein dynamics Protein folding Coarse-grained modeling 
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Notes

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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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Laboratory of Theory of Biopolymers, Faculty of ChemistryUniversity of WarsawWarsawPoland

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