Highlights•High-throughput docking of small molecules is very successful in hit identification,
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …

Structure-based drug discovery (SBDD) is becoming an essential tool in assisting fast and
cost-efficient lead discovery and optimization. The application of rational, structure-based …

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 …

Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Conspectus This Account highlights recent advances and discusses major challenges in
investigations of cryptic (hidden) binding sites by molecular simulations. Cryptic binding …

Molecular dynamics (MD) simulations are useful tools for structure-based drug design. We
review recent publications in which explicit solvent MD was used at the initial or final stages …

BCL6 was initially discovered as an oncogene in B-cell lymphomas, where it drives the
malignant phenotype by repressing proliferation and DNA damage checkpoints and …

The discovery of bioactive molecules is an expensive and time-consuming process and new
strategies are continuously searched for in order to optimize this process. Virtual Screening …

A quantitative characterization of the binding properties of drug fragments to a target protein
is an important component of a fragment-based drug discovery program. Fragments typically …

Protein-protein interactions (PPIs) underlie the majority of biological processes, signaling,
and disease. Approaches to modulate PPIs with small molecules have therefore attracted …