An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.

ABSTRACT: Coarse-grained or mesoscopic models of proteins and the corresponding force fields are of great importance because they enable us to reduce the folding simulation time by several orders of magnitude compared to the all-atom approach and, consequently, reach the millisecond time scale of simulations. In the coarse-grained UNRES model for simulations of protein structure and dynamics, developed by our group, each amino acid residue is represented by a united side chain and a united peptide group located in the middle between the two neighboring alpha-carbon atoms, which assist only in the definition of the geometry. The prototype of the UNRES force field has been defined as a potential of mean force or restricted free-energy function corresponding to averaging out the degrees of freedom not

SUBMITTER: Shen H 

PROVIDER: S-EPMC2766665 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature