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Introducing the Wolfram ProteinVisualization paclet!

Posted 10 months ago

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POSTED BY: Soutick Saha
14 Replies

6-4-23 How does this apply to any given amino acid sequence - is it possible to run any sequence? What length _ how many amino acids? Does it calculated energies of any conformations? Any other descriptive and instructional details? How does one typically run the packet installations for iMac? Apologies< I’m new at Mathematica.

Hi Paul,

Thanks a lot for your message. Here are the answers to your questions :

Q1. How does this apply to any given amino acid sequence - is it possible to run any sequence?

Ans : Unfortunately no. In general all functions in the paclet only plots for structures present in the RCSB Protein Data Bank (https://www.rcsb.org/) or if you have the structure file in .cif.gz or .pdb format.

Q2. What length _ how many amino acids?

Ans : That completely depends on the structure you want to explore. There is no upper or lower bound to it.

Q3. Does it calculated energies of any conformations?

Ans : No. This paclet basically uses existing protein structure data to do various things, that does involve some computations like dihedral angles (https://en.wikipedia.org/wiki/Dihedral_angle), distance matrix and so on, but no energy calculations.

Q4. Any other descriptive and instructional details?

Ans: All instructions can be found in individual documentation pages for functions (See : https://resources.wolframcloud.com/PacletRepository/resources/WolframChemistry/ProteinVisualization/guide/ProteinVisualization.html) and click on individual links to explore the documentations.

Q5. How does one typically run the packet installations for iMac?

Ans : Just download the notebook attach to this post, run it and get started.

Hope this answers your questions.

Best, Soutick

POSTED BY: Soutick Saha

See if you can find the paclet on a remote server using PacletFindRemote: enter image description here

POSTED BY: Robert Nachbar

Thanks Bob!

POSTED BY: Soutick Saha
Posted 10 months ago

That's so cool! PacletFindRemote[] is a great shortcut to searching the known Paclet sites yourself!

POSTED BY: Chase Marangu
Posted 10 months ago

This is amazing! The same day as you, I posted a graph theory -related post myself, about word ladders. Having multiple visualization tools, in my post this included adjacency matrices as well as several network diagrams with different arrangements of the vertices, can be great for developing intuitions about the structure of graphs.

Network diagrams are popular, but adjacency matrices and related plots like your ProteinContactMap are often overlooked tools that can help give intuition about the structure graphs.

POSTED BY: Chase Marangu

Hi Chase,

Thank you! I believe the functions ResidueDistanceGraph, ProteinContactGraphPlot and ProteinContactMap will help elucidate the gross geometric signatures of a protein structure :)!

POSTED BY: Soutick Saha

This is really very nice! Great work, Soutick! Thank you for sharing it.

Mathematica has such untapped potential in the computational biology world.

Recently I had a need to map RNA sequencing reads to the human genome, and unfortunately Mathematica is not up to the challenge. Too much data and too slow. One thing that would be super nice for scientists exploring the human genome is to have a performant implementation of the fm-index available in Mathematica. Perhaps you might bring this up in internal meetings.

Thanks again for sharing. I may be able to use this in some of my undergraduate courses.

Todd

POSTED BY: Todd Allen

Hi Todd,

Thank you so much for the kind words! I am excited to know that you will be using my paclet for your courses. Hope you find it useful!

One of the leading motivations to make this paclet was to use it to explain complex structural biology concepts to students. In particular the ProteinBackboneAtomPlot, AmidePlanePlot and DihedralAnglePlot was written with educational applications in mind. Let me know if you have any questions about using my paclet for your course.

Regarding your query -

"Recently I had a need to map RNA sequencing reads to the human genome, and unfortunately Mathematica is not up to the challenge. Too much data and too slow. One thing that would be super nice for scientists exploring the human genome is to have a performant implementation of the fm-index available in Mathematica. Perhaps you might bring this up in internal meetings."

I am new to the Language myself, so don't have answer to this question at the moment. Nonetheless I have contacted the relevant person in the company who might know more about this and waiting for a response.

I will get back to you once I hear anything. Hope that is okay.

Best, Soutick

POSTED BY: Soutick Saha

Soutick,

I just tried to install and use your paclet, and I was greeted with this error message:

enter image description here

Did I do something wrong? Todd

POSTED BY: Todd Allen

Hi Todd,

I am not sure what the problem is here. The command - PacletInstall["WolframChemistry/ProteinVisualization"] seems right and it works for me.

enter image description here

You might want to Quit your kernel and try running it again. Let me know if it is still giving error.

POSTED BY: Soutick Saha

Hi Soutick,

I was able to solve my problem by executing:

PacletSiteUpdate[PacletSites[]]

After running that snippet of code, everything worked fine!

Todd

POSTED BY: Todd Allen

That sounds great Todd. Hope you find it useful. Let me know if you have more questions.

POSTED BY: Soutick Saha

enter image description here -- you have earned Featured Contributor Badge enter image description here Your exceptional post has been selected for our editorial column Staff Picks http://wolfr.am/StaffPicks and Your Profile is now distinguished by a Featured Contributor Badge and is displayed on the Featured Contributor Board. Thank you!

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