Introduction: Computational modeling has rapidly advanced over the last decades. Recently,
machine learning has emerged as a powerful and cost-effective strategy to learn from …

Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-
physical (alchemical) thermodynamic cycles have shown great promise for structure-based …

We assess costs and efficiency of state-of-the-art high-performance cloud computing and
compare the results to traditional on-premises compute clusters. Our use case is atomistic …

With the ability to transport cargo molecules across cell membranes with low toxicity, cell-
penetrating peptides (CPPs) have become promising candidates for next generation peptide …

We review recent progress in optimal control in stochastic thermodynamics. Theoretical
advances provide in-depth insight into minimum-dissipation control with either full or limited …

Approaches for computing small molecule binding free energies based on molecular
simulations are now regularly being employed by academic and industry practitioners to …

Blocking the association between the severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) spike protein receptor-binding domain (RBD) and the human angiotensin …

The prediction of mutation‐induced free‐energy changes in protein thermostability or protein–
protein binding is of particular interest in the fields of protein design, biotechnology, and …

The Coulomb interactions in molecular simulations are inherently approximated due to the
finite size of the molecular box sizes amenable to current-day compute power. Several …

Alchemical relative binding free energy calculations have recently found important
applications in drug optimization. A series of congeneric compounds are generated from a …