Structure-based virtual screening (VS) is a widely used approach that employs the
knowledge of the three-dimensional structure of the target of interest in the design of new …

Highlights•Currently, developing a market-approved drug costs a staggering $2.6 billion.•In
silico methods have become an important strategy for narrowing down on promising lead …

Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

This manuscript presents the latest algorithmic and methodological developments to the
structure‐based design program DOCK 6.7 focused on an updated internal energy function …

Transcription factors recognize specific genomic sequences to regulate complex gene-
expression programs. Although it is well-established that transcription factors bind to specific …

It is now plausible to dock libraries of 10 million molecules against targets over several days
or weeks. When the molecules screened are commercially available, they may be rapidly …

Flexible modeling of the protein–ligand complex structure is a fundamental challenge for in
silico drug development. Recent studies have improved commonly used docking tools by …

Chemical probes that form a covalent bond with a protein target often show enhanced
selectivity, potency, and utility for biological studies. Despite these advantages, protein …

Cellular processes are the product of interactions between biomolecules, which associate to
form biologically active complexes. These interactions are mediated by intermolecular …

The discovery of drug-like molecules that bind pockets in proteins that are not present in
crystallographic structures yet exert allosteric control over activity has generated great …