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1

General discussions (Q&As) / Re: From DNA sequence to DNA structure

« on: November 20, 2009, 12:24:16 am »

Thanks for your reply, for me a newbie, I do learn a lot in this new field from this forum and your kindly reply.
I've wrote a mail to Dr. Olson. I hope that I could get 3DNA 2.0 to test my data again.

2

General discussions (Q&As) / Re: From DNA sequence to DNA structure

« on: November 19, 2009, 03:21:28 am »

I figured out an approach to deal with my question. However, I'm not sure it is good (proper) or not. Could anyone give me some comment or suggestion please?
1. I used only dinucleotide shift, slide, rise, tilt, roll and twist parameters that download from DiProDB, but ignored Shear, Stretch, Stagger, Buckle, Prop-Tw and Opening.
2. I wrote a small program to generate a base step parameter file from DNA sequence just like the bp_step.par in X3DNA example.
3. I use rebuild program to build a 3D model by using the base step parameter file in step 2.
   (rebuild -atomic M1_sense.3dna M1_sense.3dna.pdb)
 
Everything works fine. But when I use SPDB Viewer to visualize my model, I found some segment did not connected well (please see Picture 2.png in attached file).
Is this problem can be fixed?
Or this is a viewer problem? I've tried JMol, but Jmol cannot show it properly.

I upload my base step parameter for reference.

Thanks

3

General discussions (Q&As) / From DNA sequence to DNA structure

« on: November 18, 2009, 03:06:33 am »

Dear All,
I'm newbie in this field, however, I did not find any topic that can answer my question.
I want to study whether a pair of genes that separated by a distance of DNA sequence would close together in 3D conformation.

So, how to use 3DNA to generate a 3D DNA double-helix structure like this: http://http://hydra.icgeb.trieste.it/~kristian/dna/images/modelit_long2.jpg from a DNA sequence?
 I've surveyed some tools like ADN-Viewer (not publicly available), model.it (can not accept long DNA).
And I've alos tried fiber, but all I got just a linear string of DNA structure like attached "Picture 1.png".

I know the "reconstruction function" in w3DNA provide a function: "Customized base-pair-step/nucleotide parameters".
But user seems have to provide all the parameters between every adjacent base pairs (dinucleotides): (example: http://http://w3dna.rutgers.edu/public/example/example_dna.txt)
So I think I need a set of general parameters to describe Shear, Stretch, Stagger, Buckle, Prop-Twist, Opening, Shift, Slide, Rise, Tilt, Roll, Twist for 16 dinucleotides.
There is a database called: DiProDB http://http://diprodb.fli-leibniz.de/ShowTable.php that already provides some parameters for dinucleotides.

Is 3DNA provide "general" parameters to reconstruct a naked double-strand DNA just like model.it did?

Thanks first.