This paper presents motif retrieval from a macromolecule or a protein by using structure comparison in 3D through an exhaustive matching analysis of secondary structures. The comparison is based on three parameters: midpoint distance (Md), axis distance (Ad) and angle (ϕ) related to a couple of SSs in 3D space. The barycenter of the motif is assigned as Reference Point (RP) and in order to find the RP related to every possible motif (instance) in the macromolecule a voting process is performed. The searched motif is compared with all possible instances having the same number of motif SSs in the macromolecule and gives a vote to the candidate barycenter for every correspondence. The point, which has the maximum number of votes, is determined as candidate RP. In this paper motifs composed by four and five secondary structures are searched. Experimental results show a good accuracy in determining the RP and hence in the retrieval of the searched motif.
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