22 citations · 41 across the 4 of their papers we have counts for
4 papers
Lost in Projection? Gaussian Filtering Recovers Hidden Conformational States
Sofia Sartore, Daniel Nagel, Georg Diez +1
To interpret molecular dynamics (MD) simulations, it is common practice to reduce the dimensionality of the molecular coordinates to a low-dimensional collective variable . Proj…
Markov-type state models to describe non-Markovian dynamics
Sofia Sartore, Franziska Teichmann, Gerhard Stock
When clustering molecular dynamics (MD) trajectories into a few metastable conformational states, the Markov state models (MSMs) assumption of timescale separation between fast int…
Towards a Benchmark for Markov State Models: The Folding of HP35
Daniel Nagel, Sofia Sartore, Gerhard Stock
Adopting a s-long molecular dynamics (MD) trajectory of the reversible folding of villin headpiece (HP35) published by D. E. Shaw Research, we recently constructed a Mark…
Selecting Features for Markov Modeling: A Case Study on HP35
Daniel Nagel, Sofia Sartore, Gerhard Stock
Markov state models represent a popular means to interpret molecular dynamics trajectories in terms of memoryless transitions between metastable conformational states. To provide a…