Abstract: The present invention is directed to systems and methods for fast and accurate structural representation and comparison of proteins. Specifically, the present invention provides a method for retrieval of a candidate set of near structural neighbors or structurally similar proteins of a query protein. The method is based on a representation of a protein structure as a “bag of words”—a collection of small disjoint backbone protein fragments. The representation allows quick comparison procedures of the query protein structure to a large number of known protein structures obtained for example, from a repository or database of proteins.

Abstract: The present invention is directed to systems and methods for fast and accurate structural representation and comparison of proteins. Specifically, the present invention provides a method for retrieval of a candidate set of near structural neighbors or structurally similar proteins of a query protein. The method is based on a representation of a protein structure as a “bag of words”—a collection of small disjoint backbone protein fragments. The representation allows quick comparison procedures of the query protein structure to a large number of known protein structures obtained for example, from a repository or database of proteins.