Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: SASA of nucleobases  (Read 361 times)

Offline Mohit Chawla

  • with-posts
  • *
  • Posts: 7
    • View Profile
SASA of nucleobases
« on: February 06, 2020, 01:35:47 am »
Hello,
May I know if we have the option in DSSR from which we can calculate the solvent accessible surface area of individual nucleobases of RNA structures?
Thanks
Mohit

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1502
    • View Profile
    • 3DNA homepage
Re: SASA of nucleobases
« Reply #1 on: February 06, 2020, 01:01:38 pm »
Hi Mohit,

No, DSSR does not provide an option to calculate solvent accessible surface area.

For such purpose, you may have a look of freesasa:

Quote
FreeSASA is a C library and command line tool for calculating Solvent Accessible Surface Area (SASA) of biomolecules. It is designed to be simple to use with defaults, but allows customization of all parameters of the calculation and provides a few different tools to analyze the results.

Best regards,

Xiang-Jun
« Last Edit: February 06, 2020, 04:57:51 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary

Offline Mohit Chawla

  • with-posts
  • *
  • Posts: 7
    • View Profile
Re: SASA of nucleobases
« Reply #2 on: February 06, 2020, 04:23:10 pm »
Hello,
Thanks, I will check it. I also found that Naccess software could also do this job.
Regards,
Mohit

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1502
    • View Profile
    • 3DNA homepage
Re: SASA of nucleobases
« Reply #3 on: February 06, 2020, 04:56:32 pm »
Yes, http://wolf.bms.umist.ac.uk/naccess is another well-known software program for SASA calculation, and I used it before. I mentioned freesasa in my previous response since it can be taken as a modern replacement of naccess.

It helps if you could share your use case with either one on RNA nucleobases.

Best regards,

Xiang-Jun
« Last Edit: February 06, 2020, 05:01:03 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary

 

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.