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Software to create protein maps


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#1 theseeker

theseeker

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Posted 16 March 2009 - 01:57 PM

Is there software that will generate nice-looking linear maps of a protein?

For example:

http://www.familialm...k/sod1gene.jpeg

Best-case scenario would be a program where I can just paste in the DNA sequence of a protein, tell it where the exons begin/end, then it would generate a nice linear map, listing "Exon1, exon 2" etc. Then I could add other features like "kinase domain" or "ATP binding pocket". And then create a sub-region (as in the link) for mutational hot-spots, highlighting specific mutations.

I know I could just make something from scratch in Powerpoint or Canvas, etc. but wondering if there might be something that will make my life easier. Mac software preferred but I can deal with Windows if necessary.

Thanks for any help.

-Seeker

#2 Paraboxa

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Posted 17 March 2009 - 02:25 AM

I don't think you can create tertiary structures from DNA sequences due to the redundancy in the genetic code. It's straightforward from primary info (amino acid sequence), though. The protein crystallography world has several programes. These are fantatsic and enable you to rotate amino acids (e.g histidine) and see the effect on binding sites etc. As for creating your own on powerpoint, sounds like a lot of work. You can "walk" along the protein from amino acid to amino acid. You can also measure bond lengths and distances between amino acids in folded states.




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