Structural analysis of proteins by structural representation and comparison of proteins
AssigneeCarmel-Haifa University Economic Corp. Ltd.
InventorsInbal Tal, Yuval Nov, Rachel Kolodny
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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.
Claims20
A system for searching structurally similar proteins, comprising:
- a first storage that maintains a library of representations of three dimensional structures of disjoint protein backbone fragments;
- a second storage that maintains macromolecular structures of a plurality of proteins, each protein structure of the plurality of proteins represented by a respective first array, wherein each first array records observation frequencies of the disjoint protein backbone fragments in each respective protein of the plurality of proteins;
- and
- a processor communicatively coupled to the first storage and second storage, wherein the processor:
- obtains a three dimensional structure of a query protein,
- transforms the three dimensional structure of the query protein to a second array that records observation frequencies of the disjoint protein backbone fragments in the query protein by comparison to the library of representations of three dimensional structures of disjoint protein backbone fragments,
- determines similarity between each of the first arrays and the second array, thereby identifying proteins in the plurality of proteins that are structurally similar to the query protein.
A method for generating a representation for the macromolecular structure of a protein of interest, comprising:
- i) acquiring a first representation of a collection of predetermined, three dimensional structure of disjoint protein backbone fragments
- ii) acquiring a second representation, wherein said second representation comprises the three dimensional structure of a plurality of backbone segments in said protein of interest;
- iii) utilizing a processor to determine the most geometrically similar protein backbone fragment in said first representation for each of said backbone segments;
- and
- iv) generating data being the observation frequencies of each most geometrically similar protein backbone fragment in said protein of interest;
- said data represents the macromolecular structure of the protein of interest.
A method for generating a database representing macromolecular structures of a plurality of proteins, comprising:
- i) acquiring a first representation of a collection of predetermined, three dimensional structure of disjoint protein backbone fragments
- ii) acquiring a second representation wherein said second representation comprises the three dimensional structure of a plurality of backbone segments in each protein of said plurality of proteins;
- iii) utilizing a processor to determine the most geometrically similar backbone fragment in said first representation for each of said backbone segments;
- and
- iv) generating data being the observation frequencies of each said most geometrically similar protein backbone fragment in each protein of said plurality of proteins;
- v) for each protein in said plurality of proteins, encoding an array maintaining said data;
- and optionally storing the array in said database.
Dependencies are inferred from the claim text.