3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: Mohit Chawla on February 06, 2020, 01:35:47 am

Title: SASA of nucleobases
Post by: Mohit Chawla 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
Title: Re: SASA of nucleobases
Post by: xiangjun 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 (https://github.com/mittinatten/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
Title: Re: SASA of nucleobases
Post by: Mohit Chawla 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
Title: Re: SASA of nucleobases
Post by: xiangjun 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 (https://github.com/mittinatten/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