Peptide folding simulations.
Developments in the design of small peptides that mimic proteins in complexity, recent advances in nanosecond time-resolved spectroscopy methods to study peptides and the development of modern, highly parallel simulation algorithms have come together to give us a detailed picture of peptide folding dynamics. Two newly implemented simulation techniques, parallel replica dynamics and replica exchange molecular dynamics, can now describe directly from simulations the kinetics and thermodynamics of peptide formation, respectively. Given these developments, the simulation community now has the tools to verify and validate simulation protocols and models (forcefields).
Gnanakaran
S
S
Theoretical Biology and Biophysics Group, Theoretical Division, T10 MS K710, Los Alamos National Laboratory, NM 87545, USA.
Nymeyer
Hugh
H
Portman
John
J
Sanbonmatsu
Kevin Y
KY
García
Angel E
AE
D003198:Computer Simulation; D008956:Models, Chemical; D009038:Motion; D010455:Peptides / Q000737:chemistry* / Q000145:classification; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013696:Temperature; D013997:Time Factors
D010455:Peptides