Sugar puckering algorithm in 3DNA

[maryatx3dna]

Sir

i would like to know which algorithm is used in calculating sugar puckers in 3DNA to understand the comparison between values obtained from other softwares.


mary

[xiangjun]

3DNA uses the formula of Altona & Sundaralingam (1972): Conformational Analysis of the Sugar Ring in Nucleosides and Nucleotides. A New Description Using the Concept of Pseudorotation [J. Am. Chem. Soc., 94(23), pp. 8205–8212].

See my blogpost "Two slightly different definitions of sugar pucker" for a newer set of formula due to Westhof & Sundaralingam (1983): A Method for the Analysis of Puckering Disorder in Five-Membered Rings: The Relative Mobilities of Furanose and Proline Rings and Their Effects on Polynucleotide and Polypeptide Backbone Flexibility. [J. Am. Chem. Soc., 105(4), pp. 970–976].

DSSR can calculate sugar puckering parameters using either of the two sets, depending on a switch. See the DSSR User Manual for details.

HTH,

Xiang-Jun

[maryatx3dna]

Thank you very much sir