Globular proteins are held together by interacting networks of amino acid residues. A
number of different structural and computational methods have been developed to …

Biochemical activity and core stability are essential properties of proteins, maintained
usually by conserved amino acids. Structural dynamics emerged in recent years as another …

Network-based models of proteins are popular tools employed to determine dynamic
features related to the folded structure. They encompass all topological and geometric …

A protein superfold is a type of protein fold that is observed in at least three distinct, non-
homologous protein families. Structural classification studies have revealed a limited …

Literature on the topological properties of folded proteins that has emerged as a field in its
own right in the past decade is reviewed. Physics-based construction of coarse-grained …

Protein structure networks (PSNs) were widely used in analyses of protein structure and
function. In this work, we analyzed and compared the characters of PSNs by different …

The total number of amino acid sequences that can fold to a target protein structure, known
as “designability”, is a fundamental property of proteins that contributes to their structure and …

We consider self-avoiding polygons in a restricted geometry, namely an infinite L× M tube in
${{\mathbb {Z}}}^{3} $. These polygons are subjected to a force f, parallel to the infinite axis …

Highly designable structures can be distinguished based on certain geometric graphical
features of the interactions, confirming the fact that the topology of a protein structure and its …

A general framework by which dynamic interactions within a protein will promote the
necessary series of structural changes, or “conformational cycle,” required for function is …