POVME: An algorithm for measuring binding-pocket volumes

Researchers engaged in computer-aided drug design often wish to measure the volume of a ligand-binding pocket in order to predict pharmacology. We have recently developed a simple algorithm, called POVME (POcket Volume MEasurer), for this purpose. POVME is Python implemented, fast, and freely available. To demonstrate its utility, we use the new algorithm to study three members of the matrix-metalloproteinase family of proteins. Despite the structural similarity of these proteins, differences in binding-pocket dynamics are easily identified.

Figure optionsDownload high-quality image (249 K)Download as PowerPoint slideResearch highlights▶ An algorithm has been developed to measure the volume of protein binding pockets. ▶ The steps of this algorithm are explained in detail. ▶ To demonstrate its utility, the algorithm is used to identify differences in the binding-pocket dynamics of three structurally similar matrix metalloproteinases.