In enzymes, the active site is the location where incoming substrates are chemically
converted to products. In some enzymes, this site is deeply buried within the core of the …

Insulin is a peptide hormone known for chiefly regulating glucose level in blood among
several other metabolic processes. Insulin remains the most effective drug for treating …

In this study, we applied steered molecular dynamics (SMD) simulations to investigate the
unbinding mechanism of nine inhibitors of the enzyme cyclin-dependent kinase 5 (CDK5) …

Understanding ligand− protein recognition and interaction processes is of primary
importance for structure-based drug design. Traditionally, several approaches combining …

The dissociation of ligands from proteins and other biomacromolecules occurs over a wide
range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far …

As shown by Jarzynski, free energy differences between equilibrium states can be
expressed in terms of the statistics of work carried out on a system during non-equilibrium …

After ATP-actin monomers assemble filaments, the ATP's γ-phosphate is hydrolyzed within
seconds and dissociates over minutes. We used all-atom molecular dynamics simulations to …

Computational simulations in biophysics describe the dynamics and functions of biological
macromolecules at the atomic level. Among motions particularly important for life are the …

We demonstrate that the binding affinity of a multichain protein–protein complex, insulin
dimer, can be accurately predicted using a streamlined route of standard binding free …

The kinetic analysis of coumarin oxidation by CYP2A6 suggested that substrate binding and
release occurred in the multiple steps and such events proceeded rapidly. However, the …