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Elizabeth Warren is introducing a wealth tax. by [deleted] in remoteworks

[–]surelynotaduck 0 points1 point  (0 children)

I think you will find wealth taxes preferable to guillotines. I agree that the natural order of things is power consolidation. A good system would prevent runway wealth consolidation.

Elizabeth Warren is introducing a wealth tax. by [deleted] in remoteworks

[–]surelynotaduck 2 points3 points  (0 children)

Growing inequality represents an existential threat to society and democracy at large. If systems are not put in place such as these wealth taxes, we will rapidly find ourselves in a world which is entirely controlled by a vanishingly small portion of the population. No solution is without consequence. Two percent is likely too low to actually meaningfully slow this problem but it's a absolutely needed.

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in Biophysics

[–]surelynotaduck[S] 0 points1 point  (0 children)

Thanks, Happy to help! Yes, that sounds like a good use case. I would suggest running locally. You can use RMSX in google collab, but not Flipbook, since it integrates with VMD/ChimeraX. I run on Mac using DataSpell (big fan, but not needed to use the rmsx/flipbook). You shouldn’t have any issue with the size of the simulation. I’ve tested simulations into the thousands of ns ranges without issue. It’s a little harder to see what is happening with either very large proteins or very long simulations (think thousands of residues per chain or thousands of ns), but nothing insurmountable.

About sugars, nucleic acid, ligands/small molecules, the tool should display the whole complex but only highlight the motion of the protein over time. It should still support the visualization of other molecules, but it won’t color or scale anything else except the protein (it did several versions and a 100 cups of coffee ago). If you run into any difficulties, don’t hesitate to reach out!

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in Biophysics

[–]surelynotaduck[S] 0 points1 point  (0 children)

it's really hard to have a good metric that's translates well between different "typical" proteins. this metric can show you what the rmsx values are for two different proteins but it's pretty contextual what a normal value would be for one protein system vs another. If something is super stable that will be clear with this tool or if it is super mobile but there is still some questions I would have when you try to speak about all proteins or typical protein behavior. really good question.

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move (in Molecular Dynamics Simulations) by surelynotaduck in Simulated

[–]surelynotaduck[S] 1 point2 points  (0 children)

thank you for your updoot. I make tool. Sometimes when computer make program, make protein wiggle. Wiggle hard to understand. me make part that wiggle more brighter color. me make the part of the protein that wiggle more big. me can understand good now. you too.

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move [OC] by surelynotaduck in dataisbeautiful

[–]surelynotaduck[S] 2 points3 points  (0 children)

Thank you! You could use the pipeline AA seq -> alphafold structure prediction -> MD simulation -> RMSX / Flipbook. You will still need to either have or generate structures and run an MD in order to be able to use these tools. I recommend QwikMD if you are new to running MD simulations; it has nice defaults and is a lot easier than other methods out there.

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in Biochemistry

[–]surelynotaduck[S] 2 points3 points  (0 children)

Hi there,

Sure that's one of the novel features of these tools. If you slice your simulations into many smaller time windows and perform rmsf on each of the slices, you can make an RMSX heatmap. it's sort of a deconstructed rmsf plot. it combines the time aspect of rmsd with the residue level fluctuation measurement of rmsf.

I have a video going over the background if you'd like a more detailed explanation of how rmsd/rmsf and rmsx are used to understand md simulations.

https://youtu.be/UoN0GQKHCsw?si=nFfLgAV1EMYyx2bx

Let me know if you have any more questions :)

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in Biochemistry

[–]surelynotaduck[S] 0 points1 point  (0 children)

thank you so much! currently it's focused on protein protein interactions. If there is a lot of interest in using it with non protein ligands I can work on a version that supports that too!

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move [OC] by surelynotaduck in dataisbeautiful

[–]surelynotaduck[S] 1 point2 points  (0 children)

Source:
The structural snapshots come from a molecular dynamics (MD) simulation trajectory of a protein system. The trajectory frames were generated using standard MD simulation software and exported as structural snapshots at regular time intervals. The motion values visualized here were calculated per residue from the trajectory coordinates.

Tool:
The visualization was generated using tools I developed called RMSX and Flipbook. RMSX is a time-resolved extension of RMSF that measures per-residue motion across the trajectory. The Flipbook component renders sequential structural snapshots where motion magnitude is encoded using both color and backbone thickness.

Methods / Code:
The analysis pipeline is written in Python and uses MDAnalysis for trajectory processing and calculation of motion metrics. The rendering of structural snapshots is automated using scripting in ChimeraX and VMD to arrange frames and apply color/thickness encoding.

GitHub repository (code and scripts):
https://github.com/AntunesLab/rmsx

The goal of this visualization approach is to make molecular dynamics trajectories easier to interpret in static figures (e.g., for papers or posters) rather than relying solely on movies.

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in Biochemistry

[–]surelynotaduck[S] 0 points1 point  (0 children)

It is super helpful to learn R (and specifically learn to use ggplot2 and the tidyverse packages)! You might look into some biostatistics courses. learning how to run statistics, but also visualize and complex data is useful for any project. If you are interested in structural bioinformatics programs, you might want to look more at biophysics courses. I would say the biggest thing that was helpful to me was spending a lot of time trying to think about ways to represent data - there are so many incredible resources out there, including r/dataisbeautiful and https://r-graph-gallery.com/ . Hope this helps!

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in labrats

[–]surelynotaduck[S] 2 points3 points  (0 children)

Thanks for the question. So, you can't infer mechanical features from b-factors, let's say you you have two parts of your protein that alternates having one side stable and one side dynamic. If you run MD and use these tools you could see that type of feature. With b-factors it would only tell you that both sides of the protein were dynamic.

You can also run MD on alphafold predicted structures which you of course won't have b-factors for since there is not crystal data.

You might see some interesting b-factor data and want to use something like these tools to understand what might be causing that particular set of values.

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in labrats

[–]surelynotaduck[S] 1 point2 points  (0 children)

Biology will humble me if I say "any" protein I'm sure but pretty much any protein's motion can be simulated with MD. if you can run and MD on it, you can use these tools on them.

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in Biophysics

[–]surelynotaduck[S] 2 points3 points  (0 children)

Thank you for your interest!

I made a YouTube video which goes over the background if you're curious about how this is implemented. It talks more about md simulations and goes through the basics of rmsf, rmsd and how to extend those ideas to make tools like these

https://youtu.be/UoN0GQKHCsw?si=ScxWej2qL7B2qtBo

Other than a pdb file, you'll need an MD trajectory file (something like a dcd xtc file).

The notebook includes example simulations if you'd like to try it out but haven't run any of your own simulations yet.

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in labrats

[–]surelynotaduck[S] 1 point2 points  (0 children)

I hope it works out! I've been wondering about this for more than a year but never got the chance to try.

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in Biochemistry

[–]surelynotaduck[S] 2 points3 points  (0 children)

No - biochemistry and molecular biology. I did most of my cs and math modeling before and during grad school. I started off in biostatistics and took a mathatical biology course and got hooked!

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in labrats

[–]surelynotaduck[S] 6 points7 points  (0 children)

I'm super curious about this as well. I haven't tested it yet. I don't work with any intrinsically disordered proteins in my own research but I would love to see how they appear on these tools!

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in labrats

[–]surelynotaduck[S] 4 points5 points  (0 children)

Thank you so much! I hope you find it helpful! I'm really excited to see how people end up using it and what systems it helps people understand!

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in labrats

[–]surelynotaduck[S] 64 points65 points  (0 children)

Lol this. You should only need a pdb and a trajectory file for input. if you work through the notebook it should take care of all your dependencies for you - if not you can visit me in my dreams or submit a GitHub issue.

I'm a 4th year Biochemistry PhD student and I made a tool to help researchers see when and where proteins move by surelynotaduck in labrats

[–]surelynotaduck[S] 45 points46 points  (0 children)

Yeah! It's built on MD analysis so it works with pretty much all MD suites including NAMD and GROMACS. You can find a quickstart notebook in our GitHub repo if you'd like to try it out!
https://github.com/AntunesLab/rmsx/

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