Binding site matching in rational drug design: algorithms and applications.

ABSTRACT: 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 pockets. Understanding the physicochemical qualities of binding pockets is essential to improve not only our basic knowledge of biological systems, but also drug development procedures. In order to quantify similarities among pockets in terms of their geometries and chemical properties, either bound ligands can be compared to one another or binding sites can be matched directly. Both perspectives routinely take advantage of computational methods including various techniques to represent and compare small molecules as well as local protein structures. In this review, we survey 12 tools widely used to matc

SUBMITTER: Naderi M 

PROVIDER: S-EPMC6954434 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature