3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: maryatx3dna on February 01, 2017, 01:46:25 am

Title: Sugar puckering algorithm in 3DNA
Post by: maryatx3dna on February 01, 2017, 01:46:25 am: 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
Title: Re: Sugar puckering algorithm in 3DNA
Post by: xiangjun on February 01, 2017, 11:04:46 am: 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 (http://x3dna.org/highlights/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 (http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf) for details.

HTH,

Xiang-Jun
Title: Re: Sugar puckering algorithm in 3DNA
Post by: maryatx3dna on February 01, 2017, 11:11:13 am: Thank you very much sir