Linear Or 2D Representation Of Protein Sequence Secondary Structure

Question

[Pals]

Could anyone please tell me if there is any program where I can define the secondary structure elements for a given sequence and get the topology in a straight line (unlike the one provided by PDBsum). Like the one shown below:

Thanks.

Answer 1

[dimkal]

try Jalview, to which you can add custom secondary structure (and other) annotations.

Answer 2

[Chris]

Depends if you're talking about secondary structure assignment or prediction. For the first one you'll need the pdb structure, the second one works on sequence alone but is less accurate. Try DSSP (from Kabsch, Sander) for assigning and e.g. PROFphd (from Rost) for prediction.

[Pals]

It's not about prediction. I have the predictions, I need to represent them manually over the sequence.

[Pals]

I do not want to predict. I have the predictions, I want to develop 2D plot (straight) out of the predictions for the sequence.

Answer 3

[Yogesh Pandit]

You can try Bio3D.

You can explore it to see if it is useful. I am not thorough with this package. But it is well documented and only a few lines of code required.

Answer 4

[Khader Shameer]

Not a ready made solution, but points that you think through:

You can write a program to do something like that using GD::* modules in Perl. You can start with GD::Simple and design a program that read your secondary structure data and provide an image as output*.

If you are not comfortable with Perl, I am sure that equivalent modules will be available in Python, Ruby or other language of your interest. All of these are port of GD graphics library coded in C.

Other option is to try if Bio::Graphics module and see if you can have a vertical layout instead of default horizontal layout. If it is possible you can quickly generate such a a figure using few lines of codes. See a Bio::Graphics HOWTO.

Other options:

If you have access to structural data (.pdb files):

• you can generate the secondary structure assignments using HERA program. See abstract here. I have used it before and it provide figures like this: See figure
• Structure based Pro-Origami
• MyDomains (easy to use tool, elegant glyphs but only available in horizontal layout). Generate figures like this: See figure

Answer 5

[Suzanne]

There is a video on secondary structure prediction of proteins in Jalview on YouTube, the link is https://youtu.be/z5cVjR9Q3Mw