2005/06/05 by Naoto Morikawa, Morikawa, Naoto
Biochemistry, Genetics and Molecular Biology · Computer Science · Mathematics · #52B99 #92D20 (primary) #Combinatorics (math.CO) #Discrete Mathematics (cs.DM) #FOS: Biological sciences #FOS: Computer and information sciences #FOS: Mathematics #Fractal and DNA sequence analysis #Genomics (q-bio.GN) #Machine Learning in Bioinformatics #Metric Geometry (math.MG) #Protein Structure and Dynamics #cs.DM #math.CO #math.MG #msc:52B99 #msc:92D20 #q-bio.GN
paper · pdf · doi:10.48550/arxiv.math/0506082
10 pages, 6 figures, 3 tables. Submitted
arxiv created 2005/06/05 · openalex publication_date 2005/06/05 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method is the correspondence between protein-folding and ``integration''. A protein is approximated by a folded tetrahedron sequence. And the binary code of a protein is obtained as the ``second derivative'' of the shape of the folded tetrahedron sequence. With this method at hand, we can extract static structural information of a protein from its gene. And we can describe the distribution of three-dimensional structures of proteins without any subjective hierarchical classification.