Alright folks, the plan went from "I'll be alright" to "OH MY GOD I MAY NOT FINISH" back to "I'll be alright".
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| When you start the next step weeks earlier |
I'm going to provide a quick crash course on what I've been doing. In order to write my paper I need a chimera of a protein to be 1) Refined by a computer 2) Refined manually 3) Simulated in MD and 4) DFI analyzed. Previously I expected the first step of my analysis to be complete around March 6th, which would have essentially screwed me over in timeline, but it turns out I don't need all 60,000 structures (which would have set me 2 weeks back). Instead I only need around 10,000 to carry on with my analysis.
So this week I focused on selecting the correct structures from step 1. I got the "scoring" of the structures back from the refinement and learned which structures were in the lowest energy state. The whole process of scoring took two days and a ton of troubleshooting, but I eventually got the data back. After selecting the data, I decided to create a fail safe incase the zam.py runs take too long. I will take the 10 or so structures to manual refinement to create the "ultimate chimera for steps 3 and 4, but just incase step 2 takes too long I will send minimized chimera 12 straight to step 3 to ensure that I have DFI data of chimeras. Friday was one crazy day. I came in at 10 to analyze the scoring data with Dr. Ozkan, we realized that the scoring algorithm was wrong. So John and I troubleshooted it and managed to get it to run. Then I manually extracted all the data from the terminals with the good old copy and paste. I had to listen to Kpop for about 2 and a half hours but I powered through it. Then at around 5pm, I started the GPU trials with the minimized chimera 12. And it ran smoothly until yesterday. I'll have to go back in and fix it on Monday.
Overall, I have step 1 complete and I will be able to secure chimeras in time for the final paper.
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| A protein model without conservation colors |
My "data analysis" is essentially in step 4. I will take the structures and run them through DFI to learn about the interactions between non conserved and conserved positions within proteins. The timeline for this is one day, in fact I think it only takes around 2 hours. But the real issue is interpreting the results. I will obtain two different representations. The first is a graph with all 600 amino acids on the x axis and the DFI score on the y axis. By placing the chimera and the original side by side I will be able to pick out trends from the analysis. The second is a 3D model with blue and red highlights for conserved and non conserved regions. It will be easy compare between the original and the chimera.
So basically the raw numbers will give me the graphs to easily identify how the non conserved and conserved regions are moving within the original and chimera proteins.
The meme of the week on the other hand is Trash Doves, a notable set of Facebook stickers. It rose to fame with one of the birds thrashing their heads up and down.
Hey ‘Shwath!
ReplyDeleteIt’s so great to hear that you are back on track regarding your schedule, and that you’ll finish your research on time! I also think that it’s good that you’re refining the chimera both by a computer and by hand, since this is an additional validity precaution. Regarding your analysis, I have no clue what DFI means. Why do you need to ensure that you have that data for your chimera proteins? Is it a software program that you are running your data through? Also, what kind of trends are you looking for? I would clarify this when writing your results. You should connect your analysis back to answering your research question, and can do so by explaining what the trends you may find may contribute to the significance of your research. It’s good that you have two clear graphs that you can interpret, though! Be sure to include these in your written Results section!
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Ashwath, my understanding is that you're trying to determine if the protein is still functional when you mutate the nonconserved positions. How will you determine that? I get that you're doing a comparison, but what exactly are you looking for in that comparison? How does protein folding fit into that part of the equation? I think the explanations in terms of the methods' functions needs to be a bit more robust.
ReplyDeleteSup 'Shwath! So first of all, I'm glad to see that despite the errors in your code of Friday (gosh do code errors stress me out!!), you were able to resolve them and finish the first part of your methods. What is the difference between refining the chimeras through a computer versus manually? Because it seems to me that refining manually will also take a lot of time (but I also don't really know what this entails, so I could just be spewing garbáge sorry). If I'm being honest, I didn't really understand what was happening in your explanation of step 4, but after reading Mrs. Haag's comment and a little google searching, I think I understand a little better. Is DFI short for dynamic flexibility index? If so, then will you basically be assessing how the various parts of the chimera proteins (whose nonconserved parts have been mutated) contribute to protein dynamics and how this compares to the regular proteins? Will the contribution to protein dynamics indicate whether the chimera protein is still functional? Like Mrs. Haag said, it's going to be imperative that you fully flesh out the theory behind DFI and what exactly this analysis will reveal, because otherwise it will be so easy for a reader to get lost and not understand the significance of your results. Once you explain this clearly, then you will be able to make great use of your graphs as they will be more intuitive to the reader. You've clearly been hard at work! Great job! (255)
ReplyDeleteHi Ashwath! You're project is sick! While I understood what was going on, I feel like you did not convey what exactly your data analysis will do or tell us. You told us "I'm going to get two things," but I want to know what those things do to answer your question. Also the analysis that you will get out honestly seems overwhelming, so how are you going to pick out information to include in your results section or how do you plan on coming to conclusions on these graphs?
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