Perspective: Markov models for long-timescale biomolecular dynamics
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Title
Perspective: Markov models for long-timescale biomolecular dynamics
Authors
Keywords
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Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 141, Issue 9, Pages 090901
Publisher
AIP Publishing
Online
2014-09-05
DOI
10.1063/1.4895044
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- (2013) Jared Ostmeyer et al. NATURE
- Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
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