Sequence dependent bp step parameters

[spreus]

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).
So I was wondering if there is a reference for the default values used by 3DNA for the different dinucleotide steps?

Best,
Søren

[spreus]

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

[xiangjun]

Hi Søren,

Thanks for your 3 posts, and I wish I could have been able to get back to you earlier. However, w3DNA 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 (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 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 does), so any comparison with other parameter sets may not be meaningful.

Xiang-Jun

[spreus]

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