Abstract:
:We accelerate protein folding in all-atom molecular dynamics simulations by introducing alternating hydrogen bond potentials as a supplement to the force field. The alternating hydrogen bond potentials result in accelerated hydrogen bond reordering, which leads to rapid formation of secondary structure elements. The method does not require knowledge of the native state but generates the potentials based on the development of the tertiary structure in the simulation. In protein folding, the formation of secondary structure elements, especially alpha-helix and beta-sheet, is very important, and we show that our method can fold both efficiently and with great speed.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Wolf MG,de Leeuw SWdoi
10.1529/biophysj.107.122192subject
Has Abstractpub_date
2008-05-15 00:00:00pages
3742-7issue
10eissn
0006-3495issn
1542-0086pii
S0006-3495(08)70377-1journal_volume
94pub_type
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