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

Allostery is the phenomenon in which a ligand binding at one site affects other sites in the
same macromolecule. Allostery has important roles in many biological processes …

Methods developed toward computational exploration of protein landscapes have become
standardized tools to assess biophysical experimental findings. They are also used on their …

Molecular dynamics (MD) and normal mode analysis (NMA) are very useful methods for
characterizing various dynamic aspects of biological macromolecules. In comparison to MD …

There have been many coarse-graining methods developed that aim to reduce the sizes of
simulated systems and their computational costs. In this work, we develop a new coarse …

Understanding the dynamics of biomolecules is the key to understanding their biological
activities. Computational methods ranging from all-atom molecular dynamics simulations to …

Key steps in the life cycle of a virus, such as the fusion event as the virus infects a host cell
and its maturation process, relate to an intricate interplay between the structure and the …

Abstract Glucose-Methanol-Choline (GMC) family enzymes are very important in catalyzing
the oxidation of a wide range of structurally diverse substrates. Enzymes that constitute the …

Understanding how much solvents influence the structures and dynamics of proteins is
important to understand functional mechanisms of solvated proteins. We propose a solvated …

PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles
in various functions. In this study, we aim to explore functional evolutionary relationship …