[Rdkit-discuss] File Conversion?

[Carl MacGentey]

Dear RDKit Discussion Group-

Is it possible to convert fasta files (DNA nucleotide sequences) into PDB 
files? I am wanting to view strands of DNA and full length genes in three 
dimensions.

Sent from Mail for Windows 10

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Re: [Rdkit-discuss] File Conversion?

[Curt Fischer]

This is not really possible.  Fasta files contain only sequence
information, not 3D structural information.

Curt

On Sun, Dec 4, 2016 at 7:00 AM, Carl MacGentey 
wrote:

> Dear RDKit Discussion Group-
>
>
>
> Is it possible to convert fasta files (DNA nucleotide sequences) into PDB
> files? I am wanting to view strands of DNA and full length genes in three
> dimensions.
>
>
>
> Sent from Mail  for
> Windows 10
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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Re: [Rdkit-discuss] File Conversion?

[Rocco Moretti]

It's not something that RDKit can do - RDKit is focused more on small
organic molecules, rather than biomacromolecules.

For DNA, if all you want is an idealized B-form double helix, there's a
number of programs out there which can take in a sequence and make an ideal
(or almost-ideal) structure from it. From what I can tell 3DNA (
http://x3dna.org/) is one of the more popular ones. There's also webservers
like 3D-DART (http://haddock.science.uu.nl/dna/DARTusage.html) which can do
similar things.

The big caveat here is that unless you explicitly specify how the DNA is
non-standard, these programs will spit out perfectly regular, rod-straight
DNA double helixes. They're not going to be able to adequately model
sequence-specific subtle irregularities and curvature on their own. Frankly
speaking, unless you're looking for a starting model for subsequent
modeling steps (e.g. for input into an MD simulation) these models will
probably not be worth much. If you're just looking at it with e.g. PyMol,
they'll be utterly uninteresting.

Regards,
-Rocco

P.S. Converting protein fastas to structures are a whole 'nother ball of
wax. If you're really interested in that, take a look at the Critical
Assessment of protein Structure Prediction competition (CASP:
http://predictioncenter.org/) for the latest state-of-the-art.

On Sun, Dec 4, 2016 at 9:00 AM, Carl MacGentey 
wrote:

> Dear RDKit Discussion Group-
>
>
>
> Is it possible to convert fasta files (DNA nucleotide sequences) into PDB
> files? I am wanting to view strands of DNA and full length genes in three
> dimensions.
>
>
>
> Sent from Mail  for
> Windows 10
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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