Structure-based drug design (SBDD) utilizes the three-dimensional geometry of proteins to
identify potential drug candidates. Traditional methods, grounded in physicochemical …

With the exponential increase in publicly available protein structures, the comparison of
protein binding sites naturally emerged as a scientific topic to explain observations or …

Generating molecules with high binding affinities to target proteins (aka structure-based
drug design) is a fundamental and challenging task in drug discovery. Recently, deep …

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 …

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 …

Designing protein-binding proteins is critical for drug discovery. However, artificial-
intelligence-based design of such proteins is challenging due to the complexity of protein …

Identifying local similarities in binding sites from distant proteins is a major hurdle to rational
drug design. We herewith present a novel method, borrowed from computer vision, adapted …

Highlights•We review the recent advances in binding site comparison approach.•We
examine its use in protein function prediction.•We discuss its uses in pharmaceutical …

Aiming at a deep understanding of fragment binding to ligandable targets, we performed a
large scale analysis of the Protein Data Bank. Binding modes of 1832 drug-like ligands and …

The ability of small molecules to interact with multiple proteins is referred to as
polypharmacology. This property is often linked to the therapeutic action of drugs but it is …