A computational approach is essential whenever the complexity of the process under study
is such that direct theoretical or experimental approaches are not viable. This is the case for …

Molecular dynamics simulation methods produce trajectories of atomic positions (and
optionally velocities and energies) as a function of time and provide a representation of the …

The Helmholtz free energy, F and the entropy, S are related thermodynamic quantities with a
special importance in structural biology. We describe the difficulties in calculating these …

We introduce a new class of collective variables which allow forming efficiently beta-sheet
structures in all-atom explicit-solvent simulations of proteins. By this approach we are able to …

In this study, we examined the folding processes of eight helical proteins (2I9M, TC5B,
1WN8, 1V4Z, 1HO2, 1HLL, 2KFE, and 1YYB) at room temperature using the explicit solvent …

PACE, a hybrid force field that couples united-atom protein models with coarse-grained (CG)
solvent (J. Chem. Theory Comput. 2010, 6, 3373), has been further optimized, aiming to …

Although it is now possible to fold peptides and miniproteins in molecular dynamics
simulations, it is well appreciated that force fields are not all transferable to different proteins …

Despite initial successes in folding of proteins by molecular simulation, it is becoming
increasingly evident that current energy functions (force fields) tend to favor either α or β …

In this work, we shed new light on a much-studied case of β-hairpin folding by means of
advanced molecular dynamics simulations. A fully atomistic description of the protein and …

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 …