Molecular dynamics (MD) simulations are ideally suited to investigate protein and peptide
plasticity and flexibility simultaneously at high spatial (atomic) and high time resolution …

Molecular dynamics (MD) and Monte Carlo (MC) simulations have emerged as a valuable
tool to investigate statistical mechanics and kinetics of biomolecules and synthetic soft …

We present a systematic study directed toward the secondary structure propensity and
sampling behavior in peptide folding simulations with eight different molecular dynamics …

We report direct folding of a 17-residue helix protein (pdb: 2I9M) by standard molecular
dynamics simulation (single trajectory) at room temperature with implicit solvent. Starting …

The gradient for the fragment molecular orbital (FMO) method interfaced with effective
fragment potentials (EFP), denoted by FMO/EFP, was developed and applied to …

The interaction between a protein and external electric field (EF) can alter its structure and
dynamical behavior, which has a potential impact on the biological function of proteins and …

Chignolin, which consists of 10 amino acids, adopts two stable states in simulations at room
temperature at 1 atm: the native and misfolded states. The sequence of chignolin is …

The propensity of amyloid-(A) peptide to self-assemble into highly ordered amyloid
structures lies at the core of their accumulation in the brain during Alzheimer's disease. By …

The minima hop** algorithm (MHOP) to find global minima on potential energy surfaces is
used for protein structure prediction. The energy surface of the protein is represented with an …

Configuration-dependent diffusion (CDD) is important for protein folding kinetics with small
thermodynamic barriers. CDD can be even more crucial in downhill folding without …