Tolerance of mutate_bases

[panosk]

Dear mr. Xiang-Jun,

I am a Bioinformatics graduate student and I am trying to construct an RNA structure because there
is not an available experimentally derived one. I have found a similar structure and I want to use mutate_bases
to change some of the bases. Also, I intend to perform energy minimization to the resulting structure after the changes.

I would like to know about the limits of this strategy. I wondered if there are areas in the structure
that are "more sensitive" to such changes.  Can I make consecutive mutations? Can I change a big area?

Thank you in advance.

Regards,
Panos

[xiangjun]

Hi Panos,

Thanks for your interesting in using 3DNA, specifically the mutate_bases program.

I would like to know about the limits of this strategy. I wondered if there are areas in the structure
that are "more sensitive" to such changes.  Can I make consecutive mutations? Can I change a big area?

The 3DNA mutate_bases program is purely 'geometrical' and you can perform as many 'mutations' as you see fit. The mutated structure may contain steric clashes or some other irregularities, and it is intended to serve as a starting point in the modeling process. You need other modeling tools (e.g. AMBER) to perform energy minimization or molecular dynamics simulations.

Since you are a "Bioinformatics graduate student", your supervisor should be able to guide you in the desired direction. As far as 3DNA goes, you can simply play around with it to see what happens. If you meet any technical problem or have something to share with the community, please does not hesitate to post back on the Forum.

Best regards,

Xiang-Jun

PS. You may find my blogpost "The 3DNA mutate_bases program is cited in Nature" relevant. It reports a use-case of the mutate_bases program in homology modeling by scientists from the Merck Research Laboratories.