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

Thanks Bob!

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.

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

Soutick,

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

Did I do something wrong? Todd

Hi Soutick,

I was able to solve my problem by executing:

PacletSiteUpdate[PacletSites[]]

After running that snippet of code, everything worked fine!

Todd

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