Heterocyclic N-oxides have emerged as potent compounds with anticancer, antibacterial,
antihypertensive, antiparasitic, anti-HIV, anti-inflammatory, herbicidal, neuroprotective, and …

Understanding the underlying physics of the binding of small-molecule ligands to protein
active sites is a key objective of computational chemistry and biology. It is widely believed …

Water molecules play a crucial role in mediating the interaction between a ligand and a
macromolecular receptor. An understanding of the nature and role of each water molecule in …

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has
prompted researchers to pivot their efforts to finding antiviral compounds and vaccines. In …

Water molecules in the active site of an enzyme occupy a complex, heterogeneous
environment, and the thermodynamic properties of active-site water are functions of position …

Crystal structure databases offer ample opportunities to derive small molecule conformation
preferences, but the derived knowledge is not systematically applied in drug discovery …

Factor Xa (fXa) is a critical serine protease situated at the confluence of the intrinsic and
extrinsic pathways of the blood coagulation cascade. FXa catalyses the conversion of …

The binding between two biomolecules is one of the most critical factors controlling many
bioprocesses. Therefore, it is of great interest to derive a reliable method to calculate the free …

A new approach, MOBILE, is presented that models protein binding-sites including bound
ligand molecules as restraints. Initially generated, homology models of the target protein are …

Efficient ligands of factor Xa usually feature a more or less preorganized central scaffold
which orients two approximately orthogonal vectors to fill the S1 and S4 pockets at the …