Protein-protein binding site identification by enumerating the configurations.

ABSTRACT:

Background

The ability to predict protein-protein binding sites has a wide range of applications, including signal transduction studies, de novo drug design, structure identification and comparison of functional sites. The interface in a complex involves two structurally matched protein subunits, and the binding sites can be predicted by identifying structural matches at protein surfaces.

Results

We propose a method which enumerates "all" the configurations (or poses) between two proteins (3D coordinates of the two subunits in a complex) and evaluates each configuration by the interaction between its components using the Atomic Contact Energy function. The enumeration is achieved efficiently by exploring a set of rigid transformations. Our approach incorporates a surface ide

SUBMITTER: Guo F 

PROVIDER: S-EPMC3478195 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature