Messages

1

RNA structures (DSSR) / Calculate base step parameters manually

« on: February 22, 2020, 02:54:32 pm »

Hi,

I am getting an unexpected dichotomy in my measurements of twist for two stacked noncanonical base pairs from molecular dynamics data. The twist values fall in two distributions separated by ~120°. See attached pdf.  When I view the frames, I do not see discontinuities.  I would like to superimpose the reference coordinate axes on my frames and visualize the twist angle that is being reported.  I have not found a place that tells me exactly how to create the appropriate axes and vectors to see this angle. Can you direct me to a paper or site that will help?

Mike Bruist

2

RNA structures (DSSR) / Noncanonical base pair standards

« on: May 26, 2019, 12:10:55 pm »

I am characterizing variations in noncanonical RNA base pairs created by molecular dynamics. I wish to have a standard against which to compare my observed pair structures. Is there a table of local base pair parameters and/or simple base pair parameters for the pairs in the twelve families of Leontis-Westhof base pairs? For example, has anyone run each of the exemplars found in the Nucleic Acid Data Bank or Bowling Green catalog (http://ndbserver.rutgers.edu/ndbmodule/services/BPCatalog/bpCatalog.html) through DSSR?

Mike Bruist