Drug development is a lengthy and challenging process that can be accelerated at early
stages by new mathematical approaches and modern computers. To address this important …

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 …

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 …

Architectures for quantum computing based on neutral atoms have risen to prominence as
candidates for both near and long-term applications. These devices are particularly well …

ProBiS (Protein Binding Sites), a local structure-based comparison algorithm, is used in the
new ProBiS-Fold web server to annotate human structures from the AlphaFold database …

We developed LiSiCA (ligand similarity using clique algorithm)–ligand-based virtual
screening software that uses a fast maximum clique algorithm to find two-and three …

Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their
corresponding holo structures (with ligands) unavailable. However, apoproteins may not …

An algorithm is said to be certifying if it outputs, together with a solution to the problem it
solves, a proof that this solution is correct. We explain how state of the art maximum clique …

Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 is a virus that belongs to
the Coronaviridae family. This group of viruses commonly causes colds but possesses a …

Identification of conserved waters in protein structures is a challenging task with applications
in molecular docking and protein stability prediction. As an alternative to computationally …