title: Inclusion of nucleic acid contribution into assessment of protein 3d-1D compatibility and prediction of binding sites for nucleic acids.
abstract: The novel three dimensional structure(3D)-amino acid sequence(1D) compatibility program, 3d-1D method has developed and expanded into protein-nucleic acid system. The environment characteristics are determined using the coordinates of backbone atoms and C beta atom. This simplified estimation allows the expanded application to monitor the change of environment class depending on different sequence alignment. This method has improved the detective performance of the different protein into the similar folds. If protein has a wide contact with nucleic acid molecule, the compatibility profile goes down in the contact region without ligand molecule. This phenomenon becomes useful to monitor the binding sites of the bulky ligand such as nucleic acid and to model the protein-nucleic acid complex.
authors.affiliation: School of Pharmaceutical Sciences, University of Shizuoka, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Fujii
authors.forename: Y
authors.initials: Y
authors.lastname: Yamagata
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D045647:DNA Glycosylases; D007256:Information Systems; D009699:N-Glycosyl Hydrolases / Q000737:chemistry / Q000378:metabolism; D009696:Nucleic Acids / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D009696:Nucleic Acids; D011506:Proteins; D045647:DNA Glycosylases; D009699:N-Glycosyl Hydrolases; C076131:DNA-3-methyladenine glycosidase II