BACKGROUND Understanding biology, particularly at the level of actionable drug
discovery, is often a matter of develo** accurate stories about how proteins work. This …

Peptide‐based drugs offer high specificity, potency, and selectivity. However, their inherent
flexibility and differences in conformational preferences between their free and bound states …

The replacement of classical force fields (FFs) with novel neural-network-based frameworks
is an emergent topic in molecular dynamics (MD) simulations. In contrast to classical FFs …

Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and
functional genome. Yet, our structural understanding of how proteins interact with DNA is …

Understanding dynamics in complex systems is challenging because there are many
degrees of freedom, and those that are most important for describing events of interest are …

Markov state models represent a popular means to interpret biomolecular processes in
terms of memoryless transitions between metastable conformational states. To gain insight …

The time-dependent relaxation of a dynamical system may exhibit a power-law behavior that
is superimposed by log-periodic oscillations. D. Sornette [Phys. Rep. 297, 239 (1998)] …

Given nonstationary data from molecular dynamics simulations, a Markovian Langevin
model is constructed that aims to reproduce the time evolution of the underlying process …

Many chemical reactions and molecular processes occur on time scales that are significantly
longer than those accessible by direct simulations. One successful approach to estimating …

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest.
Computational modeling and virtual screening are a well established step in the rational …