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With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman-Wunsch approach and a raw PB substitutiondoi:10.1093/nar/gkr333 pmid:21586582 pmcid:PMC3125758 fatcat:hzpydg2n6vbk5lsi2w4fj64fxi