All-atom generalized-ensemble simulations of small proteins.
We give an overview of some generalized-ensemble techniques that have proven successful in all-atom simulations of proteins. We show that these techniques enable efficient investigations of secondary structure formation and folding in peptides and small proteins. Results are presented for various alanine-based artificial peptides and a small protein, the 36-residued villin headpiece subdomain (HP-36). Our results indicate that all-atom simulations of proteins may be more restricted by the accuracy of the present energy functions than by the efficiency of the search algorithms.
Kinnear
Brian S
BS
Portland Technology Development, Intel Corp., Hilisboro, OR 97124, USA.
Jarrold
Martin F
MF
Hansmann
Ulrich H E
UH
D003198:Computer Simulation; D008958:Models, Molecular; D016900:Neurofilament Proteins / Q000737:chemistry; D010446:Peptide Fragments / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013696:Temperature
D016900:Neurofilament Proteins; D010446:Peptide Fragments; D010455:Peptides; D011506:Proteins; C115223:villin headpiece subdomain peptide; C019529:polyalanine; C036501:polyvaline; C011080:polyglycine