This article reviews the fundamentals of variational transition state theory (VTST), its recent
theoretical development, and some modern applications. The theoretical methods reviewed …

Computationally driven engineering of proteins aims to allow them to withstand an extended
range of conditions and to mediate modified or novel functions. Therefore, it is crucial to the …

The SARS-CoV-2 main protease (Mpro) is essential for replication of the virus responsible
for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate …

Vibrational strong coupling (VSC) has recently emerged as a completely new tool for
influencing chemical reactivity. It harnesses electromagnetic vacuum fluctuations through …

Resistance to antibiotics is a public health crisis. Although carbapenems are less
susceptible to resistance than other β-lactam antibiotics, β-lactamases mediating resistance …

Here we report a computational method to improve efficiency of a de novo designed Kemp
eliminase enzyme KE15, by identifying mutations that enhance electric fields and chemical …

HIV protease (HIVPR) is a key target in AIDS therapeutics. All ten FDA-approved drugs that
compete with substrates in binding to this dimeric enzyme's active site have become …

The origin of the enzyme's powerful role in accelerating chemical reactions is one of the
most critical and still widely discussed questions. It is already accepted that enzymes impose …

Enzyme design faces challenges related to the implementation of the basic principles that
govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic …

In enzyme mechanistic studies and mutant design, it is highly desirable to know the
individual residue contributions to the reaction free energy and barrier. In this work, we show …