Oreola Donini

TL;DR: A historical perspective on the application of molecular dynamics to biological macromolecules is presented and recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed for the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories.

TL;DR: Noncovalent interactions appear ubiquitously in biology, but here the authors confine ourselves to review only noncovalents interactions between protein and protein, protein and ligand, and protein and nucleic acids.

TL;DR: A computational approach which combines high-level ab initio quantum mechanical calculations with classical free energy calculations is presented, leading to the conclusion that one need not invoke special concepts such as "low-barrier hydrogen bonds" or "pK(a) matching" to explain enzyme catalysis.

TL;DR: An extension of the MM/PB/SA methodology is presented which allows us to calculate the relative binding energies of six known nanomolar carboxylate ligands of MMP-1 and is able to rank the neutral and charged ligands correctly.

TL;DR: In this article, quantum mechanical-free energy (QM-FE) calculations were performed for the formation of the enolate-imidazole complex from the reactants, as well as for the further formation of an enol-IMidazolate system.