Antibiotic resistance is a threat to the global health infrastructure. The evolutionary changes in bacterial enzymes present themselves in the form of infections that are more difficult to treat. One such class of enzymes is the class D β-lactamases (DBLs) with their unique active site…
_Ab initio_ molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of generalized gradient approximation (GGA)…
Biased molecular dynamics methods are widely used to accelerate transitions between metastable states and for computing the underlying free energy landscapes…
Collective variable based enhanced sampling techniques and global tempering methods are widely used for accelerating barrier-crossing events and enhancing conformational sampling in molecular dynamics simulations…
Exploration and computation of free energy surfaces of chemical reactions are pivotal to computationally predicting reaction mechanisms, pathways, and kinetics…