Abstract 3D pharmacophore models are three‐dimensional ensembles of chemically
defined interactions of a ligand in its bioactive conformation. They represent an elegant way …

Highlights•Which molecular dynamics (MD) techniques are available for drug design?•How
is MD used to investigate ligand–macromolecule complexes?•How are MD studies applied …

Computational approaches are useful tools to interpret and guide experiments to expedite
the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based …

FTMap is a computational mapping server that identifies binding hot spots of
macromolecules—ie, regions of the surface with major contributions to the ligand-binding …

A pharmacophore describes the framework of molecular features that are vital for the
biological activity of a compound. Pharmacophore models are built by using the structural …

Protein dynamics play an important role in small molecule binding and can pose a
significant challenge in the identification of potential binding sites. Cryptic binding sites have …

Identifying binding hotspots on protein surfaces is of prime interest in structure-based drug
discovery, either to assess the tractability of pursuing a protein target or to drive improved …

Predicting relative protein–ligand binding affinities is a central pillar of lead optimization
efforts in structure-based drug design. The site identification by ligand competitive saturation …

Chemical fragment cosolvent sampling techniques have become a versatile tool in ligand-
protein binding prediction. Site-identification by ligand competitive saturation (SILCS) is one …

An increasing number of medically important proteins are challenging drug targets because
their binding sites are too shallow or too polar, are cryptic and thus not detectable without a …