Motivation: The ability to predict binding profiles for an arbitrary protein can significantly
improve the areas of drug discovery, lead optimization and protein function prediction. At …

Identifying a protein's functional sites is an important step towards characterizing its
molecular function. Numerous structure-and sequence-based methods have been …

Protein target identification for drugs or drug candidates is essential for avoiding unwanted
side-effects evoked by off targets. Additionally, it opens the route for drug repurposing and …

Protein binding sites are the places where molecular interactions occur. Thus, the analysis
of protein binding sites is of crucial importance to understand the biological processes …

Similarities in binding cavities attract attention for the prediction and doptimization of ligand
selectivity. Glinca and Klebe propose a clustering based on physicochemical properties of …

Automated prediction of protein active sites is essential for large-scale protein function
prediction, classification, and druggability estimates. In this work, we present DoGSite, a new …

In the field of medicinal chemistry there is increasing focus on identifying key proteins whose
biochemical functions can firmly be linked to serious diseases. Such proteins become …

We benchmarked the ability of comparative computational approaches to correctly
discriminate protein pairs sharing a common active ligand (positive protein pairs) from …

Methods for comparing protein binding sites are frequently validated on data sets of pockets
that were obtained simply by extracting the protein area next to the bound ligands. With this …

Identification of potential ligand‐binding pockets is an initial step in receptor‐based drug
design. While many geometric or energy‐based binding‐site prediction methods …