Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Author Topic: SASA of nucleobases  (Read 19757 times)

Offline Mohit Chawla

  • non-commercial
  • with-posts
  • *
  • Posts: 9
    • 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: 1650
    • 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 »

Offline Mohit Chawla

  • non-commercial
  • with-posts
  • *
  • Posts: 9
    • 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: 1650
    • 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 »

 

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University