2D structure of a custom protein (not in any databases) from a PDB file.
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8 weeks ago
Hansen_869 ▴ 60

Hi! I'm looking for a tool that can convert the 3D protein structure of a custom PDB file (not in any databases) into a 2D representation. So that the protein is laid out flat and "opened up" so you can see all loops, beta sheets and helices. Is there any such software out there?

Thanks!

Tool Pymol PDB protein structure • 666 views
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8 weeks ago
Wayne ★ 1.7k

There's a number of options available depending specifically on what you seek:

Notes about Khan et al., 2018 'ProLego: tool for extracting and visualizing topological modules in protein structures' and the ProLego server in the hopes they help others be careful & use the correct resources, perhaps carefully share code and servers better so that others may use the sites and tools you create. Or maybe spurs the authors or BMC Bioinformatics to update / fix things now or BMC Bioinformatics better set editorial policies in the future, or reviewers to make sure policies encouraging sharing of the science are adhered to or that what is backing the paper can be assessed:

While the paper makes this look like a nice tool. Accessing it and what it can do is anything but easy. In fact a few years after publishing it, it is practically a minefield. Starting with the sites listed under 'Availability and requirements' section in Khan et al., 2018 'ProLego: tool for extracting and visualizing topological modules in protein structures'. Trying to use either the links 'Project home page' or what is listed just above as 'Studied protein datasets' listed in the project site seemingly hijacks my browser to a multitude of varying URLs that say there's a security issue and that I need to install their extension. The correct link seems to be http://proteinlego.indirag.org/ and that should have been in the paper or updated by the publisher.

Circling back to the 'Availability and requirements' section, this should be where at least some of the code for what is billed as a "pythonic" solution should be shared. There are much better ways to archive share code that helps insure their utility going forward. And that provides adaptability to people looking to use your code and build on it. Please look into GitHub and other repositories or OSF.

Clicking on 'Data' in the navigation bar gets a server error. Were these the referred to "Studied protein datasets ... listed in the project site" under the 'Availability of data and materials' section?

Entering 1ema at Compute ProLego Topology from Proteins [PDB] under 'Get PDB from RCSB' leads to 'Server Error (500)'.

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Hi Wayne! Thanks for your elaborate response. I have now looked at the tools and it seems that they're all based on existing proteins. I failed to mention (corrected now), that this is for a custom protein (my own). Hence, it is not in any databases yet. Any such tools for that purpose?

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Yes, two of the three mention uploading your own protein. (Although, I'm not confident ProLego server actually works now. It was supposed to do that functionality at one time.) PDDsum let's you use 'Generate' on the server. Or you can even download it. I put that in the post already & for further emphasis I just highlighted some of the appropriate parts.

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Ah, you are right! Thank you.

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8 weeks ago
Jiyao Wang ▴ 310

You can also try out iCn3D. After you load your custom PDB via the menu "File > Open File > PDB Files", you can click the menu "Analysis > 2D Cartoon > Helix/Sheet Level" to get the projection of secondary structures from 3D to 2D. Here is one example with the URL https://structure.ncbi.nlm.nih.gov/icn3d/share.html?5iZSHNbXcJisp7gQ6 :