The ability of small molecules to interact with multiple proteins is commonly referred to as
polypharmacology. The now widely accepted polypharmacology of drugs is of particular …

Abstract Protein–protein interactions (PPIs), such as protein–protein inhibitor, antibody–
antigen complex, and supercomplexes play diverse and important roles in cells. Recent …

A new algorithm for finding a maximum clique in an undirected graph is described. An
approximate coloring algorithm has been improved and used to provide bounds to the size …

Most small molecule drugs interact with unintended, often unknown, biological targets and
these off-target interactions may lead to both preclinical and clinical toxic events. Undesired …

Modern rational drug design not only deals with the search for ligands binding to interesting
and promising validated targets but also aims to identify the function and ligands of yet …

A plethora of databases exist online that can assist in in silico chemical or drug safety
assessment. However, a systematic review and grouping of databases, based on purpose …

The automated comparison of protein-ligand binding sites provides useful insights into yet
unexplored site similarities. Various stages of computational and chemical biology research …

Location and properties of ligand binding sites provide important information to uncover
protein functions and to direct structure-based drug design approaches. However, as …

The process of drug design requires the initial identification of compounds that bind their
targets with high affinity and selectivity. Advances in generative modeling of small molecules …

The binding of drugs and reagents to off-targets is well-known. Whereas many off-targets are
related to the primary target by sequence and fold, many ligands bind to unrelated pairs of …