3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: spreus on May 17, 2011, 01:18:07 pm

Title: Sequence dependent bp step parameters
Post by: spreus on May 17, 2011, 01:18:07 pm: Hi

I notice that when rebuilding B-DNA structures using w3DNA the default sequence dependent bp step parameters differ from what I can find in the DiProDB (http://diprodb.fli-leibniz.de/ShowTable.php (http://diprodb.fli-leibniz.de/ShowTable.php)).
So I was wondering if there is a reference for the default values used by 3DNA for the different dinucleotide steps?

Best,
Søren
Title: Re: Sequence dependent bp step parameters
Post by: spreus on May 18, 2011, 07:11:04 am: I should probably specify my question better:
The "default" bp step parameter values I'm referring to are those used by the "B-DNA (generic)" rebuilding option in w3DNA.

All the best,
Søren
Title: Re: Sequence dependent bp step parameters
Post by: xiangjun on May 19, 2011, 10:38:41 pm: Hi Søren,

Thanks for your 3 posts, and I wish I could have been able to get back to you earlier. However, w3DNA (http://http://3dna.rutgers.edu:8080/forum/viewforum.php?f=10) is out of my reach: I am not that familiar with the internal details of w3DNA, no access to the server, no time to devote to it (http://http://xiang-jun.blogspot.com/2009/07/on-maintaining-3dna-forum.html) (unfortunately).

3DNA itself does not have "default" bp step parameter values for rebuilding. The "B-DNA (generic)" option you mentioned may refer to the fiber (http://http://xiang-jun.blogspot.com/2009/10/fiber-models-in-3dna.html) models. To verify, run "[mono:3nnrwi6s]fiber[/mono:3nnrwi6s]" to generate a B-DNA (default) model, and then "[mono:3nnrwi6s]analyze[/mono:3nnrwi6s]" it to see the parameters involved. Moreover, 3DNA does not have a compilation of various bending models (as SCHNArP (http://http://3dna.rutgers.edu:8080/forum/viewforum.php?f=9) does), so any comparison with other parameter sets may not be meaningful.

Xiang-Jun
Title: Re: Sequence dependent bp step parameters
Post by: spreus on May 24, 2011, 08:15:59 am: Hi Xiang-Jun

Ah okay, I think I get it now. For anyone else looking for the same information:
B-DNA (generic) is the fiber model from Calf Thymus by Arnott & coworkers.
B-DNA (generic alternate) is a fiber model of Premilat and Albiser.

References for the above models are provided in table 4 of the 2003 NAR paper on 3DNA.

Thanks,
Søren