After conquering the atomic structure about a century ago, chemists have been largely
interested in understanding the concept of chemical bond and the formation of a molecule …

It has long been recognized that certain sites within a protein, such as sites in the protein
core or catalytic residues in enzymes, are evolutionarily more conserved than other sites …

Proteins are the most important biomolecules for living organisms. The understanding of
protein structure, function, dynamics, and transport is one of the most challenging tasks in …

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie
their biological functions. Recent studies indicate that these dynamic properties are …

Topology is at the very heart of chemistry. This stems from the fact that chemical thought,
since its prescientific alchemic origins, focused on the mutual relations between different …

Background Popular bioinformatics approaches for studying protein functional dynamics
include comparisons of crystallographic structures, molecular dynamics simulations and …

Recently, we saw a dramatic increase in the number of researches that rely on coarse-
grained (CG) simulations for large biomolecules. Here, first, we briefly describe recently …

Understanding molecular mechanisms underlying the complexity of allosteric regulation in
proteins has attracted considerable attention in drug discovery due to the benefits and …

The three-dimensional structure of a protein is formed and maintained by the noncovalent
interactions among the amino-acid residues of the polypeptide chain. These interactions can …

The allosteric mechanism plays a key role in cellular functions of several PDZ domain
proteins (PDZs) and is directly linked to pharmaceutical applications; however, it is a …