Phys. Rev. E 78, 061905 (2008) [4 pages]Folding proteins by first-passage-times-optimized replica exchangeReceived 6 June 2008; published 3 December 2008 Replica exchange simulations have become the method of choice in computational protein science, but they still often do not allow an efficient sampling of low-energy protein configurations. Here, we reconstruct replica flow in the temperature ladder from first passage times and use it for temperature optimization, thereby maximizing sampling. The method is applied in simulations of folding thermodynamics for a number of proteins starting from the pentapeptide Met-enkephalin, through the 36-residue HP-36, up to the 67-residue protein GS-α3W. © 2008 The American Physical Society URL:
http://link.aps.org/doi/10.1103/PhysRevE.78.061905
DOI:
10.1103/PhysRevE.78.061905
PACS:
87.10.−e, 05.10.Ln, 02.70.Rr, 02.70.Tt
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