5 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…
Contact cluster modeling of allosteric communication in PDZ domains
Emanuel Dorbath, Fabian Rudolf, Adnan Gulzar +1
Allostery, the intriguing phenomenon of long-range communication between distant sites in proteins, plays a central role in biomolecular regulation and signal transduction. While i…
Recovering Hidden Degrees of Freedom Using Gaussian Processes
Georg Diez, Nele Dethloff, Gerhard Stock
Dimensionality reduction represents a crucial step in extracting meaningful insights from Molecular Dynamics (MD) simulations. Conventional approaches, including linear methods suc…
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…
Allosteric communication mediated by protein contact clusters: A dynamical model
Ahmed A. A. I. Ali, Emanuel Dorbath, Gerhard Stock
Allostery refers to the puzzling phenomenon of long-range communication between distant sites in proteins. Despite its importance in biomolecular regulation and signal transduction…