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 of the …

We have developed a new system, ProBiS-Dock, which can be used to determine the different
types of protein binding sites for small ligands. The binding sites identified this way are …

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 …

Motivation: Exploitation of locally similar 3D patterns of physicochemical properties on the
surface of a protein for detection of binding sites that may lack sequence and global structural …

Research efforts are placing an ever increasing emphasis on identifying signal transduction
pathways related to the chemopreventive activity of curcumin. Its anticarcinogenic effects are …

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-dimensional …

The ProBiS web server is a web server for detection of structurally similar binding sites in the
PDB and for local pairwise alignment of protein structures. In this article, we present a new …

A new exact parallel maximum clique algorithm MaxCliquePara, which finds the maximum
clique (the fully connected subgraph) in undirected general and protein graphs, is presented. …

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 …

Small-molecule docking has proven to be invaluable for drug design and discovery. However,
existing docking methods have several limitations such as improper treatment of the …