Three-dimensional protein structures, whether determined experimentally or theoretically,
are often too low resolution. In this mini-review, we outline the computational methods for …

Reduced computer modeling of proteins now has a history of about 30 years. In spite of the
enormous increase in computing abilities, reduced models are still very important tools for …

The prediction of protein structure from sequence remains a major unsolved problem in
biology. The most successful protein structure prediction methods make use of a divide-and …

Protein structures are classically described as composed of two regular states, the α-helices
and the β-strands and one non-regular and variable state, the coil. Nonetheless, this simple …

We compared the modes of interaction between protein-peptide interfaces and those
observed within monomeric proteins and found surprisingly few differences. Over 65% of …

Background The hierarchical and partially redundant nature of protein structures justifies the
definition of frequently occurring conformations of short fragments as' states'. Collections of …

High-resolution structures of proteins remain the most valuable source for understanding
their function in the cell and provide leads for drug design. Since the availability of sufficient …

As modeling of changes in backbone conformation still lacks a computationally efficient
solution, we developed a discretisation of the conformational states accessible to the protein …

Energy functions are crucial ingredients of protein tertiary structure prediction methods.
Assessing the quality of energy functions is therefore of prime importance. It requires the …

Finding structural similarities between proteins often helps reveal shared functionality, which
otherwise might not be detected by native sequence information alone. Such similarity is …