State of the art in studying protein folding and protein structure prediction using molecular dynamics methods.
This study presents an overview of the state of the art in using molecular dynamics methods to simulate protein folding and in the end game of protein structure prediction. In principle, these methods should allow the highest level of detail possible and the highest accuracy, but they are limited by both the accuracy of the force field used in the simulation and the sampling possible in the available computer time. We describe current capabilities in running the simulations longer and more efficiently.
Lee
M R
MR
Department of Pharmaceutical Chemistry, University of CA, San Francisco, CA, USA.
Duan
Y
Y
Kollman
P A
PA
D002352:Carrier Proteins / Q000737:chemistry*; D003198:Computer Simulation; D008840:Microfilament Proteins / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
D002352:Carrier Proteins; D008840:Microfilament Proteins; D011506:Proteins; C026615:villin