Ankyrin Repeat Identification by Graph Spectral Analysis

Structure based identification of Ankyrin repeats by graph spectral approach
A Protein Contact Network (PCN) is constructed from a 3D protein structure as input by considering Cα atoms of amino acids as nodes and an edge drawn between them if the distance between the Cα atoms is below a predefined threshold (~7Å), capturing backbone and non-covalent interactions. This connectivity information is represented in the adjacency matrix. The repeat copies are predicted based on the conserved pattern in the eigenvector profile corresponding to the largest eigen value of adjacency matrix (eigenvector centrality) and secondary structure information from STRIDE database.

(a) The 3D protein structure, and (b) corresponding PCN for a designed ankyrin repeat protein 1N0R.




Related publication: Chakrabarty B, Parekh N: Identifying tandem Ankyrin repeats in protein structures. BMC Bioinformatics 2014, 15:6599.


Contact: Broto Chakrabarty and Dr. Nita Parekh,
Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology-Hyderabad