Abstract Structure-based virtual screening plays an important role in drug discovery and
complements other screening approaches. In general, protein crystal structures are …

Molecular docking, which is the indispensable emphasis in predicting binding conformations
and energies of ligands to receptors, constructs the high-throughput virtual screening …

Some water molecules in binding sites are important for intermolecular interactions and
stability. The way binding site explicit water molecules are dealt with affects the diversity and …

Human cytosolic sulfotransferases (SULTs) transfer the sulfuryl moiety (-SO3) from activated
sulfate [3′-phosphoadenosine 5′-phosphosulfate (PAPS)] to the hydroxyls and primary …

The use of selective inhibitors of monoamine oxidase A (MAO-A) and B (MAO-B) holds a
therapeutic relevance in the treatment of depressive disorders and Parkinson's disease …

The last step of cysteine biosynthesis in bacteria and plants is catalyzed by O-acetylserine
sulfhydrylase. In bacteria, two isozymes, O-acetylserine sulfhydrylase-A and O-acetylserine …

Docking programs that use scoring functions to estimate binding affinities of small molecules
to biological targets are widely applied in drug design and drug screening with partial …

S4MPLE is a conformational sampling tool, based on a hybrid genetic algorithm, simulating
one (conformer enumeration) or more molecules (docking). Energy calculations are based …

HADDOCK is one of the few docking programs that can explicitly account for water
molecules in the docking process. Its solvated docking protocol starts from hydrated …

A key challenge in structure-based discovery is accounting for modulation of protein-ligand
interactions by ordered and bulk solvent. To investigate this, we compared ligand binding to …