Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G4 Structures · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: Sugar puckering algorithm in 3DNA  (Read 2082 times)

Offline maryatx3dna

  • regular
  • *
  • Posts: 27
    • View Profile
Sugar puckering algorithm in 3DNA
« 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

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1427
    • View Profile
    • 3DNA homepage
Re: Sugar puckering algorithm in 3DNA
« Reply #1 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" 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
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline maryatx3dna

  • regular
  • *
  • Posts: 27
    • View Profile
Re: Sugar puckering algorithm in 3DNA
« Reply #2 on: February 01, 2017, 11:11:13 am »
Thank you very much sir

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.