Metadynamics is a powerful technique for enhancing sampling in molecular dynamics
simulations and reconstructing the free‐energy surface as a function of few selected …

Metadynamics calculations allow investigating structure, plasticity, and energetics in a
variety of biological processes spanning from molecular docking to protein folding. Recent …

We review a selection of methods for performing enhanced sampling in molecular dynamics
simulations. We consider methods based on collective variable biasing and on tempering …

Peptidyl-prolyl isomerases catalyze the conversion between cis and trans isomers of proline.
The cyclophilin family of peptidyl-prolyl isomerases is well known for being the target of the …

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several
features with larger globular proteins. Although the system has been intensively investigated …

The binding mechanism of a peptide substrate (Thr-Ile-Met-Met-Gln-Arg, cleavage site p2-
NC of the viral polyprotein) to wild-type HIV-1 protease has been investigated by 1.6 μs …

Functioning proteins do not remain fixed in a unique structure, but instead they sample a
range of conformations facilitated by motions within the protein. Even in the native state, a …

Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins
and in the regulation of their functions. Different families of enzymes, known as “peptidyl …

Preorganization of large, directionally oriented, electric fields inside protein active sites has
been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may …

Bias-Exchange Metadynamics is a powerful technique that can be used for reconstructing
the free energy and for enhancing the conformational search in complex biological systems …