Markov state models (MSMs) based on molecular dynamics (MD) simulations are routinely
employed to study protein folding, however, their application to functional conformational …

Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding
have long been considered a holy grail of computational biology. Due to the large system …

Markov (state) models (MSMs) and related models of molecular kinetics have recently
received a surge of interest as they can systematically reconcile simulation data from either …

Protein kinases are dynamically regulated signaling proteins that act as switches in the cell
by phosphorylating target proteins. To establish a framework for analyzing linkages between …

Biomolecules adopt a dynamic ensemble of conformations, each with the potential to
interact with binding partners or perform the chemical reactions required for a multitude of …

The study of molecular evolution at the level of protein-coding genes often entails comparing
large datasets of sequences to infer their evolutionary relationships. Despite the importance …

Cryptic allosteric sites—transient pockets in a folded protein that are invisible to
conventional experiments but can alter enzymatic activity via allosteric communication with …

Molecular recognition is determined by the structure and dynamics of both a protein and its
ligand, but it is difficult to directly assess the role of each of these players. In this study, we …

Amyloid fibril deposits of the intrinsically disordered hIAPP peptide are found in 95% of type
II diabetes patients, and the aggregation of this peptide is suggested to induce apoptotic cell …

Conformational changes underpin function and encode complex biomolecular mechanisms.
Gaining atomic-level detail of how such changes occur has the potential to reveal these …