Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …

The limitations associated with natural enzyme catalysis have triggered the rise of the field of
protein engineering. Traditional rational design was based on the analysis of protein …

The selective removal of undesired or damaged mitochondria by autophagy, known as
mitophagy, is crucial for cellular homoeostasis, and prevents tumour diffusion …

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

Abstract A mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode
Analysis (ENM-NMA)-based strategy (ie PSN-ENM) was developed to investigate structural …

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to
the dynamics of proteins. If properly analyzed, this information can lead to new insights …

Extracting dynamical pairwise correlations and identifying key residues from large molecular
dynamics trajectories or normal-mode analysis of coarse-grained models are important for …

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 …

Amino acid networks (AANs) are undirected networks consisting of amino acid residues and
their interactions in three-dimensional protein structures. The analysis of AANs provides …

In the last years, a growing interest has been gathering around the ability of Molecular
Dynamics (MD) to provide insight into the paths of long-range structural communication in …