The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

Molecular dynamics simulations have emerged as a powerful tool to study biological
systems at varied length and timescales. The conventional all-atom molecular dynamics …

Molecular dynamics with coarse-grained models is nowadays extensively used to simulate
biomolecular systems at large time and size scales, compared to those accessible to all …

Abstract The UNited RESidue (UNRES) force field was tested in the 14th Community Wide
Experiment on the Critical Assessment of Techniques for Protein Structure Prediction …

Over the past few years, many molecules such as monoclonal antibodies, affibodies,
nanobodies, and small compounds have been designed and tested as inhibitors of PD-1/PD …

The unfolded state of proteins presents many challenges to elucidate the structural basis for
biological function. This state is characterized by a large degree of structural heterogeneity …

Intrinsically disordered proteins (IDPs) contain more charged amino acids than folded
proteins, resulting in a lack of hydrophobic core (s) and a tendency to adopt rapidly …

Motivation The majority of the proteins in living organisms occur as homo-or hetero-
multimeric structures. Although there are many tools to predict the structures of single-chain …

In this chapter the scale-consistent approach to the derivation of coarse-grained force fields
developed in our laboratory is presented, in which the effective energy function originates …

With the advance of experimental procedures obtaining chemical crosslinking information is
becoming a fast and routine practice. Information on crosslinks can greatly enhance the …