My methodology will be pretty chill probably. I gonna start off by preparing LacI with several different mutations determined from other studies I've looked at. Then I'll run an REMD simulation on these proteins, simulating the mutated protein at several different temperatures. REMD is just the program I will be using. After that, I will introduce a random brownian kick which will send a reaction wave down the molecule. After the wave is sent through the molecule, I will use a DFI analysis to evaluate the change of molecule positioning. Then I plan to define what changes I am looking for in order to better understand the procedure. It shouldn't be too bad, but who knows anything is possible at this point.
But I am also looking to include a lay audience so I will have to avoid many of the pitfalls of the research papers I have read, which includes technical language, reliance on credentials, no limitation discussion, and a lack of explanation and justification.
Overall, I am very confident in my method because it is similar to one of my professor's papers. The random brownian kick and DFI analysis will help me analyze the reactions of the LacI protein. Hopefully i will be able to obtain meaningful results. However, I will have to justify and explicate the methods thoroughly because the technical information can bog down the reader and hurt the understanding of the project. I am also unsure of what I am going to define as a "significant change" within the protein structure. I will have to consult with my PSF 3rd floor professor because she has a good understanding of the changes in protein functionality. I am also unsure of the timeline required for my project, but I am sure the data will be collected in a timely fashion. Another challenge I face is converting technical terms into readable sentences for the everyday man. I hope to correct the short comings of science professors with an understandable paper.
Ashwath -- I want to reinforce the idea that you need to get a handle on the timeline. I would consult with your professor as soon as possible, as the feasibility of your project is reliant on a schedule that fits within our timeline. If the timeline isn't feasible, you'll need to work with your professor to tweak what you're doing to make it work.
ReplyDeleteHey Ashwath!
ReplyDeleteFirst off, your weekly memes are so dank that they are beyond my comprehension (I think this is a good thing?). I love that you've taken the time to understand those wild research papers! It's definitely going to pay off at the end.
I had a few questions:
1. What are REMD simulations (also, what does REMD stand for?)?
2. Since you are using the very methods to Ozkan and her past research, what would you say is the most unique part of your primary research? I think this question is really important to ask... If you have a convincing answer, emphasize this throughout your paper and blog posts more -- you're doing some amazing protein folding comp bio, so don't sell yourself short!
Anyways, keep up the dank memes and terty protein folding sims. As always, we keep it fresh at the PSF 3rd floor... am i right??
Awesome work!
YP
(153)
Hey Ashwizzle,
ReplyDeleteI agree with Yash that there was some terms that made me feel dumb because I couldn't understand like REMD simulations and the brownian kick? But also, I am not really familiar with your project, but I guess this is what you meant when you have to explain terms more simply.
I think in the beginning of your methods you could credit the papers you took inspiration from and justify why you used their methods. I agree that justifying the importance of your primary research is really important in your case due to there being similar studies with similar methods.
I am proud of you for reading so many complicated papers but ashamed of your extensive knowledge of memes that will literally be obsolete in the next few years (when you are out in the real world with real people and the memes are dead)?
Sunskruthi Krishna
(145)