Long-timescale molecular dynamics simulations of protein structure and function.
Molecular dynamics simulations allow for atomic-level characterization of biomolecular processes such as the conformational transitions associated with protein function. The computational demands of such simulations, however, have historically prevented them from reaching the microsecond and greater timescales on which these events often occur. Recent advances in algorithms, software, and computer hardware have made microsecond-timescale simulations with tens of thousands of atoms practical, with millisecond-timescale simulations on the horizon. This review outlines these advances in high-performance molecular dynamics simulation and discusses recent applications to studies of protein dynamics and function as well as experimental validation of the underlying computational models.
D. E. Shaw Research, New York, NY 10036, USA.
John L
JL
Klepeis
Kresten
K
Lindorff-Larsen
Ron O
RO
Dror
David E
DE
Shaw
D003198:Computer Simulation; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D013329:Structure-Activity Relationship; D013997:Time Factors
D011506:Proteins