At distances shorter than equilibrium, electrostatic interactions seem to be a more robust
indicator of relative molecular dimer stability than more accurate electronic structure …

Abstract Changes in solvation of ligand and receptor molecules during docking contribute
essentially to the total energy of the binding process. In aqueous solution, the exposure of …

In small molecule docking, the scoring and ranking of generated conformations is an
important, though still not a completely resolved problem. Rescoring schemes often improve …

Motivation: Interfacial water, which plays an important role in mediating biomolecular
interactions, has been neglected in the modelling of biomolecular complexes. Methods: We …

Correctly ranking protein–ligand interactions with respect to overall free energy of binding is
a grand challenge for virtual drug design. Here we compare the performance of various …

Identifying chemical starting points is a vital first step in small molecule drug discovery and
can take significant time and money. For this reason, computational approaches to virtual …

Protein–protein interactions (PPIs) are essential, and modulating their function through PPI-
targeted drugs is an important research field. PPI sites are shallow protein surfaces readily …

Protein–ligand binding is a key biological process at the molecular level. The identification
and characterization of small-molecule binding sites on therapeutically relevant proteins …

Accurate protein binding structure determination presents a great challenge to both
experiment and theory. Here, in this work, we propose a new DOX protocol which combines …

In the framework of the 2018 Drug Design Data Resource grand challenge 4, blinded
predictions on relative binding free energy were performed for a set of 39 ligands of the …