Parallel tempering simulations of HP-36.
We report results from all-atom Monte Carlo simulations of the 36-residue villin headpiece subdomain HP-36. Protein-solvent interactions are approximated by an implicit solvent model. The parallel tempering is used to overcome the problem of slow convergence in low-temperature protein simulations. Our results show that this technique allows one to sample native-like structures of small proteins and points out the need for improved energy functions.
Lin
Chai-Yu
CY
Institute of Physics, Academia Sinica, Taipei, Taiwan.
Hu
Chin-Kun
CK
Hansmann
Ulrich H E
UH
D000465:Algorithms; D008958:Models, Molecular; D009010:Monte Carlo Method; D016900:Neurofilament Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D013696:Temperature; D013816:Thermodynamics
D016900:Neurofilament Proteins; D010446:Peptide Fragments; C115223:villin headpiece subdomain peptide