SASA of nucleobases

[Mohit Chawla]

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

[xiangjun]

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:

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

[Mohit Chawla]

Hello,
Thanks, I will check it. I also found that Naccess software could also do this job.
Regards,
Mohit

[xiangjun]

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