Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics
Date
2013- Citations
- CrossRef - Citation Indexes: 17
- PubMed - Citation Indexes: 8
- Scopus - Citation Indexes: 18
- Captures
- Mendeley - Readers: 38
publications
17
supporting
0
mentioning
24
contrasting
0
Smart Citations17
0
24
0
Citing PublicationsSupportingMentioningContrasting
See how this article has been cited at scite.ai
scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.
xmlui.mirage2.itemSummaryView.MetaData
Show full item recordAbstract
We compare the efficiency of multicanonical and replica exchange molecular dynamics for the sampling of folding/unfolding events in simulations of proteins with end-to-end beta-sheet. In Go-model simulations of the 75-residue MNK6, we observe improvement factors of 30 in the number of folding/unfolding events of multicanonical molecular dynamics over replica exchange molecular dynamics. As an application, we use this enhanced sampling to study the folding landscape of the 36-residue DS119 with an all-atom physical force field and implicit solvent. Here, we find that the rate-limiting step is the formation of the central helix that then provides a scaffold for the parallel beta-sheet formed by the two chain ends.
