Protein Modeling C

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eagerlearner102
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Re: Protein Modeling C

Postby eagerlearner102 » February 25th, 2019, 8:05 pm

I do have a foundation in biochemistry. However, I would like to know more about it in detail. Which chapters do you suggest me to go over? I only have 5 days left XP.
2019 events: Protein Modeling, Sounds of Music, Fermi Questions
Other scientific pursuits: USNCO, PDB video challenge coming up!
Competition: 2019 Northern California Bay Area Regional
Fermi Questions: 2nd
Sounds of Music: 4th
Protein Modeling: 9th :?

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eagerlearner102
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Re: Protein Modeling C

Postby eagerlearner102 » February 26th, 2019, 7:08 am

Also, aside from reading the research paper by Yang and Patel for AcrIIA4 and watching videos on MSOE, what other resources did you guys use to study for CRISPR?
2019 events: Protein Modeling, Sounds of Music, Fermi Questions
Other scientific pursuits: USNCO, PDB video challenge coming up!
Competition: 2019 Northern California Bay Area Regional
Fermi Questions: 2nd
Sounds of Music: 4th
Protein Modeling: 9th :?

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What Are Judges Looking Form In Pre-Builds and On site builds?

Postby NovaBro » February 26th, 2019, 8:00 am

Every time my team and I get our test results, we never got back our grading rubric for our Pre-Builds or On site builds. I am wondering what Judges are looking for more specifically in these Pre-Builds and On Site Builds.

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Re: What Are Judges Looking Form In Pre-Builds and On site builds?

Postby CookiePie1 » February 26th, 2019, 10:01 am

NovaBro wrote:Every time my team and I get our test results, we never got back our grading rubric for our Pre-Builds or On site builds. I am wondering what Judges are looking for more specifically in these Pre-Builds and On Site Builds.


You're not really supposed to have the rubric/know what the judges are looking for. I think part of the reason that the Prebuild weighting was dropped was because some teams got their hands on the rubric when they weren't supposed to. Just do the best you can.
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2019 Events: Thermodynamics, Protein Modeling, Mission Possible, Wright Stuff

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Re: Protein Modeling C

Postby JoeyC » February 26th, 2019, 1:29 pm

Some people were going to get their hands on the rubric eventually, if not almost certainly. I have, and I never ever specifically tried to.
This website: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5595222/ gives many side chains and residue lengths that can go for extra credit. (as well as give much needed knowledge of AcrIIA4's inner workings)
Plus it's all up to perception. They look for folds and loops, and correct starting and end points, correct chirality of alpha helices and correct amount of turns, etc.
However, it doesn't mater how good the model is if your judges misgrade it, and they will (as a rule) always do this. :cry:
Unless they're a veteran of the event many fold, most people can't grade a protein correctly for the life of them (even I get confused, though I've done this event at 5 or 6 competitions now).
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Re: Protein Modeling C

Postby eagerlearner102 » February 27th, 2019, 8:14 pm

The research paper talks a lot about binary and ternary complex of sgRNA bound Spycas9. What is the major difference between the 2?
2019 events: Protein Modeling, Sounds of Music, Fermi Questions
Other scientific pursuits: USNCO, PDB video challenge coming up!
Competition: 2019 Northern California Bay Area Regional
Fermi Questions: 2nd
Sounds of Music: 4th
Protein Modeling: 9th :?

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Re: Protein Modeling C

Postby ReallyConfused » February 27th, 2019, 10:26 pm

Hi guys, I am frantically trying to get my pre-build model built and I am utterly confused. Do we need to literally put a mark for every amino acid? Also, when I viewed the protein, it seemed pretty small and only had 3-5 alpha helices. Is this right?
Thanks!

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Re: Protein Modeling C

Postby JoeyC » February 28th, 2019, 3:51 am

Yes. You do not need to mark every amino acid. It is recommended, but no one should take off points for it. (though I wouldn't consider 3-5 alpha helices small :P )
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Re: Protein Modeling C

Postby CookiePie1 » February 28th, 2019, 7:40 am

JoeyC wrote:Yes. You do not need to mark every amino acid. It is recommended, but no one should take off points for it. (though I wouldn't consider 3-5 alpha helices small :P )


While you don't need to, it is still a good practice, and for 85 residues, should only take about 3-5 minutes. Use a sharpie. It is very difficult to accurately build a model without knowing where each specific amino acid is. It will also help when you start to add sidechains and creative additions.
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2019 Events: Thermodynamics, Protein Modeling, Mission Possible, Wright Stuff

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Re: Protein Modeling C

Postby ReallyConfused » February 28th, 2019, 10:39 am

Thank you for your help! When you say "mark" the amino acids, does that mean like putting a push pin for every one? i thought about doing that but worry that it might get too crowded

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Re: Protein Modeling C

Postby ReallyConfused » February 28th, 2019, 10:58 am

Oh wait I just looked at previous protein models and I think I understand now. Thanks!

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Re: Protein Modeling C

Postby TheMysteriousMapMan » March 1st, 2019, 7:00 am

Hi all!

My coach just assigned me to be the third member of Protein Modeling. The other two and I have decided that I will focus on the test portion, as that is more of my forté. As I am new to this event, and biology events in general, where should I start studying? What should I know about CRISPR? Like I said, I know only what I learned in Bio classes as I don't normally do biology-focused events, so assume I know nothing.

Thanks for your help, in advance!

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Re: Protein Modeling C

Postby eagerlearner102 » March 1st, 2019, 9:14 am

Go on http://cbm.msoe.edu/scienceOlympiad/ to get a good foundation on CRISPR. Once you are able to lecture about CRISPR, read the 2 research papers in DETAIL. I mean in detail as in know the exact residues, knowing which domains, and perhaps the methods they used in the research paper (SEC, enzymatic assays, etc.) Focus on the Yang and Patel research paper more on the other one because I took around 5 practice tests and there was more weight on the Yang and Patel one.
For the harder ones like MIT invitational that I practiced on, I noticed that these concepts were literally found on Klein Organic Chemistry textbook chapter 25 for amino acids. I also read MIT OCW lecture notes 5.07 and 7.012 about it just to get a better understanding.
2019 events: Protein Modeling, Sounds of Music, Fermi Questions
Other scientific pursuits: USNCO, PDB video challenge coming up!
Competition: 2019 Northern California Bay Area Regional
Fermi Questions: 2nd
Sounds of Music: 4th
Protein Modeling: 9th :?

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Re: Protein Modeling C

Postby eagerlearner102 » March 1st, 2019, 9:16 am

There is an awesome video here to memorize the 20 amino acids properties and categories + abbreviations:
https://www.youtube.com/watch?v=m130s94pMjE

Once you memorize that, you have a basic understanding.
You should also have a good understanding of how DNA works.
For an interactive CRISPR, that can be found here:
https://www.hhmi.org/biointeractive/cri ... plications
Hope that helps! Good luck!
2019 events: Protein Modeling, Sounds of Music, Fermi Questions
Other scientific pursuits: USNCO, PDB video challenge coming up!
Competition: 2019 Northern California Bay Area Regional
Fermi Questions: 2nd
Sounds of Music: 4th
Protein Modeling: 9th :?

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Re: Protein Modeling C

Postby jocoboxo » March 1st, 2019, 9:23 am

Hey everyone,

when I read the articles, how do I know what's important and exactly where on the anti-CRISPR protein it should be?


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