Protein Modeling C

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TheMysteriousMapMan
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Re: Protein Modeling C

Postby TheMysteriousMapMan » March 1st, 2019, 10:10 am

eagerlearner102 wrote: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!
eagerlearner102 wrote: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.


Thanks! This looks like it will really help!

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Re: Protein Modeling C

Postby eagerlearner102 » March 1st, 2019, 5:15 pm

For the on site build is it on MSOE or do they use the JMOL program? If it is the JMOL program, isn't it the same functions as MSOE?
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Re: Protein Modeling C

Postby CookiePie1 » March 1st, 2019, 5:23 pm

eagerlearner102 wrote:For the on site build is it on MSOE or do they use the JMOL program? If it is the JMOL program, isn't it the same functions as MSOE?


It's an either/or. The syntax is the same, so it shouldn't be an issue either way. I think the jmol offline version is meant to be a backup.
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Re: Protein Modeling C

Postby eagerlearner102 » March 1st, 2019, 8:18 pm

For experienced Protein Modeling people, how did you manage to finish building the on site protein within the time limit while maintaining accuracy? Our group didn't practice a lot and seems to be a bit slow.
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Re: Protein Modeling C

Postby JoeyC » March 2nd, 2019, 5:49 am

You practice a lot. Usually, the main problem I have is running out of material (because I make sections too big), but I can just refold the protein tighter in ~5 minutes. Speed is the key; trying to get it perfect the first time is usually a lost cause (for me at least). Also, only one person should be folding it, and only one.
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Re: Protein Modeling C

Postby banilmd » March 3rd, 2019, 10:52 am

eagerlearner102 wrote:Did any of your regionals say that the prebuild is not even counted as part of the score? I am participating in the Bay Area regional on March 2nd and the director said that it wouldn't be considered. I feel so upset because my partners and I spent quite a bit of time on it.

I just competed at my regional competition, and the pre-build was taken out completely for us as well.

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Re: Protein Modeling C

Postby freed2003 » March 3rd, 2019, 11:25 am

It wasn't removed for regionals, but it has been for socal state
does anyone know the rationale behind it? Im guessing it's cause having something prebuild be so much of your score is kinda unfair
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Re: Protein Modeling C

Postby eagerlearner102 » March 3rd, 2019, 12:39 pm

TheMysteriousMapMan wrote:
eagerlearner102 wrote: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!
eagerlearner102 wrote: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.


Thanks! This looks like it will really help!

Also study RNA structure so you know the difference. that was on the regional test for me as well as knowing JMOL pretty well.
2019 events: Protein Modeling, Sounds of Music, Fermi Questions
Other scientific pursuits: USNCO, PDB Video Challenge, DNA Day (???)
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 voisinet22 » March 5th, 2019, 9:05 am

banilmd wrote:
eagerlearner102 wrote:Did any of your regionals say that the prebuild is not even counted as part of the score? I am participating in the Bay Area regional on March 2nd and the director said that it wouldn't be considered. I feel so upset because my partners and I spent quite a bit of time on it.

I just competed at my regional competition, and the pre-build was taken out completely for us as well.


Where are you finding that it is/isn't included in your regionals? Seems strange to include it in invites but not regionals..

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Re: Protein Modeling C

Postby TheMysteriousMapMan » March 6th, 2019, 12:44 pm

Thanks eagerlearner and all for the info! What would you recommend I put on my cheat sheet, and what would you recommend I memorize?

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Re: Protein Modeling C

Postby robloxparodies » March 10th, 2019, 12:45 pm

Hey guys, I finished my protein model for regionals but I have trouble trying to find ideas for "creative additions" to it. Does anyone know any good resources to get ideas for such additions? One person on this forum mentioned papers to look at but I have trouble finding them.
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Re: Protein Modeling C

Postby olhs4n6 » March 10th, 2019, 3:40 pm

robloxparodies wrote:Hey guys, I finished my protein model for regionals but I have trouble trying to find ideas for "creative additions" to it. Does anyone know any good resources to get ideas for such additions? One person on this forum mentioned papers to look at but I have trouble finding them.



I used the paper here.

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Re: Protein Modeling C

Postby Person » March 10th, 2019, 3:45 pm

olhs4n6 wrote:
robloxparodies wrote:Hey guys, I finished my protein model for regionals but I have trouble trying to find ideas for "creative additions" to it. Does anyone know any good resources to get ideas for such additions? One person on this forum mentioned papers to look at but I have trouble finding them.



I used the paper here.


And the other recommended paper is here.
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Re: Protein Modeling C

Postby adaline16 » March 10th, 2019, 7:14 pm

Hi everyone,
Where can I get access to the practice tests, such as the MIT one, or the Princeton one someone mentioned beforehand? Thanks!

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Re: Protein Modeling C

Postby Person » March 10th, 2019, 7:26 pm

adaline16 wrote:Hi everyone,
Where can I get access to the practice tests, such as the MIT one, or the Princeton one someone mentioned beforehand? Thanks!


MIT

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