title: Defining topological equivalences in macromolecules.
abstract: We describe a completely automated and objective method for defining topological equivalents in macromolecules. The method is based on well established techniques for identifying topologically and topographically equivalent atoms in small molecules and has been used in structural alignment of proteins and RNA molecules, and to extract fragments of molecules (protein secondary structures and RNA and DNA double helices) from structural databases consistent with some specified template structure.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Leeds, UK.
authors.forename: N
authors.initials: N
authors.lastname: Subbarao
authors.forename: I
authors.initials: I
authors.lastname: Haneef
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry; D006454:Hemoglobins / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009113:Muramidase / Q000737:chemistry; D009696:Nucleic Acids / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D012689:Sequence Homology, Nucleic Acid; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry
chemical_list: D004268:DNA-Binding Proteins; D006454:Hemoglobins; D009696:Nucleic Acids; D011506:Proteins; D012313:RNA; D004247:DNA; D013762:Tetrahydrofolate Dehydrogenase; D009113:Muramidase