Simulations of a small protein in a specifically designed generalized ensemble.
We describe a variant of the generalized-ensemble approach that allows faster simulations for special classes of proteins. We test this technique for an all-atom model of the 36-residue protein HP-36. The dependence of various thermodynamic quantities on small modifications of the solvent representation is explored. Configurations with a root-mean square deviation of less than 4 A to the experimentally determined structure are observed.
Department of Physics, Michigan Technological University, Houghton, Michigan 49931-1295, USA. hansmann@mtu.edu
Ulrich H E
UH
Hansmann
D000465:Algorithms; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D016900:Neurofilament Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry*; D013696:Temperature
D016900:Neurofilament Proteins; D010446:Peptide Fragments; D012997:Solvents; C115223:villin headpiece subdomain peptide