Organic chemists tend to consider the conformation of compounds as a consequence of
repulsive steric interactions. In other words,“the steric effect” means “repulsive” in many …

This is a sequel to the previous Perspective “The CH–π hydrogen bond in chemistry.
Conformation, supramolecules, optical resolution and interactions involving carbohydrates” …

HIV-1 protease remains an important anti-AIDS drug target. Although it has been known that
ligand binding induces large conformational changes in the protease, the dynamic aspects …

Proteins are not static but are flexible molecules that can adopt many different
conformations. The HIV-1 protease is an important target for the development of therapies to …

HIV maturation requires multiple cleavage of long polyprotein chains into functional proteins
that include the viral protease itself. Initial cleavage by the protease dimer occurs from within …

Accurate calculation of important thermodynamic properties, such as macromolecular
binding free energies, is one of the principal goals of molecular dynamics simulations …

Hydrophobic residues outside the active site of HIV-1 protease frequently mutate in patients
undergoing protease inhibitor therapy; however, the mechanism by which these mutations …

The main-protease (Mpro) catalyzes a crucial step for the SARS-CoV-2 life cycle. The recent
SARS-CoV-2 presents the main protease (MCoV2pro) with 12 mutations compared to SARS …

HIV-1 protease is an essential enzyme in the life cycle of the HIV-1 virus. The conformational
dynamics of the flap region of the protease is critical for the ligand binding mechanism, as …

We analyze the encounter of a peptide substrate with the native HIV-1 protease, the
mechanism of substrate incorporation in the binding cleft, and the dissociation of products …