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

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

Soutick,

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

Did I do something wrong? Todd

See if you can find the paclet on a remote server using PacletFindRemote:

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

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

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