Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model

Methods Mol Biol. 2014:1137:235-50. doi: 10.1007/978-1-4939-0366-5_16.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Internet
  • Models, Molecular
  • Molecular Dynamics Simulation*
  • Protein Conformation*
  • Protein Folding*
  • Proteins / chemistry*
  • Software*

Substances

  • Proteins