Interactions between proteins and small molecules are critical for biological functions. These
interactions often occur in small cavities within protein structures, known as ligand-binding …

The majority of biological processes involve the association of proteins or binding of other
ligands to proteins. The accurate prediction of putative binding sites on the protein surface …

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 …

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 …

A new web portal for the CHARMM macromolecular modeling package, CHARMMing
(CHARMM interface and graphics, http://www. charmming. org), is presented. This tool …

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 …

Background Identification of the residues in protein-protein interaction sites has a significant
impact in problems such as drug discovery. Motivated by the observation that the set of …

Computational prediction of residues that participate in protein-protein interactions is a
difficult task, and state of the art methods have shown only limited success in this arena. One …

In order to identify the locations of metal ions in the binding sites of proteins, we have
developed a method named the MADE (MAcromolecular DEnsity and Structure Analysis) …

A web server, ProBiS, freely available at http://probis. cmm. ki. si, is presented. This provides
access to the program ProBiS (Protein Binding Sites), which detects protein binding sites …