title: Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model.
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.
authors.affiliation: Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Jamroz
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kolinski
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kmiecik
mesh_terms: D000465:Algorithms; D020407:Internet; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins