Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …

Biological systems are by nature multiscale, consisting of subsystems that factor into
progressively smaller units in a deeply hierarchical structure. At any level of the hierarchy …

Traditionally, protein structures have been analysed by the secondary structure architecture
and fold arrangement. An alternative approach that has shown promise is modelling …

The vast majority of theoretically possible polypeptide chains do not fold, let alone confer
function. Hence, protein evolution from preexisting building blocks has clear potential …

Proteins are highly dynamic entities attaining a myriad of different conformations. Protein
side chains change their states during dynamics, causing clashes that are propagated at …

The emergence of novel proteins, beyond these that can be readily made by duplication and
recombination of preexisting domains, is elusive. De novo emergence from random …

Network theory is now a method of choice to gain insights in understanding protein structure,
folding and function. In combination with molecular dynamics (MD) simulations, it is an …

Weak molecular interactions play an important role in protein structure and function.
Computational tools that identify weak molecular interactions are, therefore, valuable for the …

Outer membrane proteins (OMPs) are the proteins in the surface of Gram-negative bacteria.
These proteins have diverse functions but a single topology: the β-barrel. Sequence …

Software tools that allow the visualization and analysis of protein interaction networks are
essential for studies in systems biology. One of the most popular network visualization tools …