One of the main challenges in molecular dynamics is overcoming the 'timescale barrier': in
many realistic molecular systems, biologically important rare transitions occur on timescales …

This paper presents a grid-based approach to model molecular association processes as an
alternative to sampling-based Markov models. Our method discretizes the six-dimensional …

Understanding mechanisms of protein folding and binding is crucial to designing their
molecular function. Molecular dynamics (MD) simulations and Markov state model (MSM) …

In this work, we investigate the role of solvent in the binding reaction of the p53
transactivation domain (TAD) peptide to its receptor MDM2. Previously, our group generated …

Abstract SHP2-E76K, a mutant encoded by the PTPN11 gene, was associated with various
solid tumors, such as lung cancer, glioblastoma, and intellectual disability. SHP2-E76K has …

Accurate and efficient simulation of the thermodynamics and kinetics of protein–ligand
interactions is crucial for computational drug discovery. Multiensemble Markov Model …

The knowledge about protein-protein interactions is rising steadily. Protein domains and
signaling proteins in particular are becoming increasingly important in the search for new …

In the last few years, Markov State Model (MSM) approaches have been widely applied to
understand folding mechanisms and predict long timescale dynamics from ensembles of …

The knowledge about protein-protein interactions is rising steadily. Protein domains and
signaling proteins in particular are becoming increasingly important in the search for new …