Understanding the structural determinants of a protein's biochemical properties, such as
activity and stability, is a major challenge in biology and medicine. Comparing computer …

The dopamine transporter (DAT) belongs to the neurotransmitter/sodium symporter (NSS)
family of membrane proteins that are responsible for reuptake of neurotransmitters from the …

Constantly advancing computer simulations of biomolecules provide huge amounts of data
that are difficult to interpret. In particular, obtaining insights into functional aspects of …

We present a maximum-caliber method for inferring transition rates of a Markov state model
(MSM) with perturbed equilibrium populations given estimates of state populations and rates …

Collective variables (CVs), when chosen judiciously, can play an important role in
recognizing rate-limiting processes and rare events in any biomolecular systems. However …

The Bayesian Inference of Conformational Populations (BICePs) algorithm reconciles
theoretical predictions of conformational state populations with sparse and/or noisy …

α-helices being the most common secondary structures found ubiquitously in proteins, have
been studied extensively for elucidating its folding dynamics and mechanism. In addition …

Markov state models (MSMs) are a powerful framework for the analysis of molecular
dynamics data sets, such as protein folding simulations, because of their straightforward …

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

The serotonin transporter (SERT) is a member of the Solute Carrier 6 (SLC6) family and is
responsible for maintaining the appropriate level of serotonin in the brain. Dysfunction of …