4 papers
From Enhanced Sampling to Human-Readable Representations of Protein Dynamics
Souvik Mondal, Michael A. Sauer, Matthias Heyden
Understanding protein conformational dynamics is essential for elucidating biological function but remains challenging due to the wide range of timescales and the complexity of col…
High-Throughput Computation of Anharmonic Low-Frequency Protein Vibrations
Michael A. Sauer, Souvik Mondal, Madeline Cano +1
At room temperature, low frequency vibrations at far-infrared frequencies are thermally excited () and not restricted to harmonic fluctuations around a single potentia…
Fast Sampling of Protein Conformational Dynamics
Michael A. Sauer, Souvik Mondal, Brandon Neff +2
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or pre…
Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations
Souvik Mondal, Michael A. Sauer, Matthias Heyden
We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anhar…