High dimensional indexing for protein structure matching using bowties

Chain Fold It is a usual way to tabulate the torsion (dihedral) angles for each residue to reconstruct protein structure using standard covalent bond length and angles. The backbone can be further represented by virtual bond between Cα-atoms. The mainchain is fully described by the virtual dihedral angle αi defined by four successive Cα atoms and the virtual bond angle. This description is used for building backbone wire models. Our Approach All the above mentioned methods are based on measuring internal Cα-Cα (residue-residue) or Cβ-Cβ (sidechain-sidechain) distances. This paper will adopt a different way by representing a protein’s structure as vectors of Cα-Cβ atoms, which has been advocated by Mckie 1995. The overall spatial relationships between the Cα-Cβ vectors will be taken into account. September 29, 2004 20:33 Proceedings Trim Size: 9.75in x 6.5in APBC05