A novel and efficient tool for locating and characterizing protein cavities and binding sites.

ABSTRACT: Systematic investigation of a protein and its binding site characteristics are crucial for designing small molecules that modulate protein functions. However, fundamental uncertainties in binding site interactions and insufficient knowledge of the properties of even well-defined binding pockets can make it difficult to design optimal drugs. Herein, we report the development and implementation of a cavity detection algorithm built with HINT toolkit functions that we are naming Vectorial Identification of Cavity Extents (VICE). This very efficient algorithm is based on geometric criteria applied to simple integer grid maps. In testing, we carried out a systematic investigation on a very diverse data set of proteins and protein-protein/protein-polynucleotide complexes for locating and charact

SUBMITTER: Tripathi A 

PROVIDER: S-EPMC2811767 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature