The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …

Nowadays, hybrid QM/MM approaches are widely used to study (supra) molecular systems
embedded in complex biological matrices. However, in their common formulation, mutual …

Enzymatic reactions play a fundamentally important role in controlling and performing most
life processes. 1-3 Thus, understanding how enzymes work has both fundamental and …

We review the standard model for de novo computational design of enzymes, which
primarily focuses on the development of an active-site geometry, composed of protein …

Conspectus The role of the enzyme's dynamic motions in catalysis is at the center of heated
contemporary debates among both theoreticians and experimentalists. Resolving these …

Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …

The site-specific solvation of the photoexcited protochlorophyllide a (Pchlide a) in methanol
solvent was investigated using the time-dependent density functional theory method for the …

This Perspective presents a review of our work and that of others in the highly controversial
topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in …