#Sugar phosphate backbone full#

Relationships to provide a full description of RNA structural motifs. RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond

#Sugar phosphate backbone software#

Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitatingД«ioinformatic comparisons. This nomenclature can also be written as a string with Modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) thatДЄre especially useful at the level of crystallographic map fitting. Since the half-nucleotides are specified by a number for ОґОµО¶ and a lowercase letter for О±ОІОіОґ, this The conformers are given two-character names that reflect the seven-angle ОґОµО¶О±ОІОіОґ combinations empirically foundДЇavorable for the sugar-to-sugar вЂњsuiteвЂќ unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for Most of these conformers represent identifiable features or roles within RNA Multidimensional dihedral angle distribution. 7Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854,ДЄ consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles.Д«y a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-filtered,.6Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, Connecticut.5Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.4School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.3School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.2Institute of Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, CZ-16610 Prague, Czech Republic.

1Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710-3711, USA.