Intrinsically disordered proteins are essential for biological processes such as cell
signalling, but are also associated to devastating diseases including Alzheimer's disease …

Generalized ensemble methods such as Hamiltonian replica exchange (HREX) and
expanded ensemble (EE) have been shown effective in free energy calculations for various …

Parallel replica exchange sampling is an extended ensemble technique often used to
accelerate the exploration of the conformational ensemble of atomistic molecular …

The weighted histogram analysis method (WHAM) and unbinned versions such as the
multistate Bennett acceptance ratio (MBAR) and unbinned WHAM (UWHAM) are widely …

Recent concurrent advances in methodology development, computer hardware and
simulation software has transformed our ability to make practical, quantitative predictions of …

We characterize the kinetics of dimer formation of the short amyloid microcrystal-forming
tetrapeptides NNQQ by constructing coarse master equations for the conformational …

A new method is proposed to calculate alchemical free-energy differences based on
molecular dynamics (MD) simulations, called the conveyor belt thermodynamic integration …

Big data is an opportunity in the emergence of novel business applications such as “Big
Data Analytics”(BDA). However, these data with non-traditional volumes create a real …

We show how accurate rates of formation and dissociation of peptide dimers can be
calculated using direct transition counting (DTC) from replica-exchange molecular dynamics …

As part of the SAMPL5 blinded experiment, we computed the absolute binding free energies
of 22 host–guest complexes employing a novel approach based on the BEDAM single …