Protein Modeling C

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Limke
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Re: Protein Modeling C

Postby Limke » February 17th, 2019, 3:40 pm

ScienceRobo wrote:I've been reading through the provided papers papers to try and find "functionally relevant features." However, they mostly discuss specific amino acids. Are there any sources that I can use to find other things I could display, or is sticking with just amino acids fine?


Sticking with amino acids is fine. Each creative addition is technically worth only 1 point (4 max) so recreating the whole file and folding binding sites from cas9 or something isn't going to earn you more points. Creative additions usually will earn full points if they are (1) sufficiently and accurately displayed (2) relevantly explained on the note card.
2019 Events: Anatomy & Physiology, Designer Genes, Forensics, Protein Modeling.

do not eat the forensics powders

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eagerlearner102
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Re: Protein Modeling C

Postby eagerlearner102 » February 18th, 2019, 12:52 pm

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.
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 :?

sdk652
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Re: Protein Modeling C

Postby sdk652 » February 20th, 2019, 4:44 pm

Per the official rules, it says that the percentage it counts for was lowered (40% to 20%). I'm pretty sure some communication went wrong.

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JoeyC
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Re: Protein Modeling C

Postby JoeyC » February 20th, 2019, 6:20 pm

Yeah, nerfing the prebuild into oblivion would be completely unfair, fortunately it wasn't. (still, losing value hurts)
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Past (Main) Events
Dynamic Planet Fast Facts, Thermodynamics, Green Generation

Current Events
Dynamic Planet Protein Modeling, Thermodynamics, More to (hopefully) come!

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Re: Protein Modeling C

Postby eagerlearner102 » February 22nd, 2019, 7:07 pm

It seems to be I am the only one who has this problem :(. I am confused why the Bay Area regional can change the national rules from 20% to 0%. Do regionals have the right to do this?
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 CookiePie1 » February 23rd, 2019, 2:31 pm

eagerlearner102 wrote:It seems to be I am the only one who has this problem :(. I am confused why the Bay Area regional can change the national rules from 20% to 0%. Do regionals have the right to do this?


Most regionals/states have rules saying that their rules clarifications/FAQs supercede the nationals rules, so according to them, ig they do have the right.
South Brunswick High School '22
2019 Events: Thermodynamics, Protein Modeling, Mission Possible

If a tree falls in a forest and no one is around to hear it, does it make a sound?

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JoeyC
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Re: Protein Modeling C

Postby JoeyC » February 23rd, 2019, 3:46 pm

I mean, half of the regionals in TX don't run all 23 events, never mind state events, and some invitationals skimp on the on site build by getting rid of it to save money.
Ohayo!
Past (Main) Events
Dynamic Planet Fast Facts, Thermodynamics, Green Generation

Current Events
Dynamic Planet Protein Modeling, Thermodynamics, More to (hopefully) come!

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Re: Protein Modeling C

Postby eagerlearner102 » February 23rd, 2019, 7:23 pm

Just wondering, how are you guys studying the biochemistry part of the test? I took some practice tests like MIT, Florida, Princeton, Long Island and I have to admit some of the questions were pretty hard (Gibbs Free Energy, total charge of peptide, psi/phi angle).
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 kevintovar28 » February 24th, 2019, 12:17 pm

Hello, so I am thoroughly confused on a few things and I was wondering if anyone could offer some clarity. For the beginning and end terminus, are they one amino acid long? And if so does that mean that it is the first amino acid and the next amino acid is #2 or? As for marking where beta sheets and helices, how can I know what amino acid it starts on? Finally, what structures are important and where can I find that information? Thanks a ton.

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Re: Protein Modeling C

Postby CookiePie1 » February 24th, 2019, 12:22 pm

kevintovar28 wrote:Hello, so I am thoroughly confused on a few things and I was wondering if anyone could offer some clarity. For the beginning and end terminus, are they one amino acid long? And if so does that mean that it is the first amino acid and the next amino acid is #2 or? As for marking where beta sheets and helices, how can I know what amino acid it starts on? Finally, what structures are important and where can I find that information? Thanks a ton.


The N and C termini are both one amino acid. They both count as one when numbering the sequences. For secondary structures, in Jmol, you can wave your mouse over the residue in question and it will tell you the number. The important structures can be found in the research papers posted on the CBM website.
South Brunswick High School '22
2019 Events: Thermodynamics, Protein Modeling, Mission Possible

If a tree falls in a forest and no one is around to hear it, does it make a sound?

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Re: Protein Modeling C

Postby kevintovar28 » February 24th, 2019, 1:35 pm

Thank you so much! Where are the research papers posted?

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Re: Protein Modeling C

Postby CookiePie1 » February 24th, 2019, 1:42 pm

kevintovar28 wrote:Thank you so much! Where are the research papers posted?


You can use this link. This site has a lot of very useful info across all aspects of the event.
South Brunswick High School '22
2019 Events: Thermodynamics, Protein Modeling, Mission Possible

If a tree falls in a forest and no one is around to hear it, does it make a sound?

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Re: Protein Modeling C

Postby bearcat09 » February 24th, 2019, 4:28 pm

I'm trying to make my model, but it says I need a mini toober that's 168 cm long (5.5 feet) and the biggest one in my kit is only 4 feet?? Am I missing a piece or just totally messing something up?

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Re: Protein Modeling C

Postby jaah5211 » February 25th, 2019, 7:31 pm

eagerlearner102 wrote:Just wondering, how are you guys studying the biochemistry part of the test? I took some practice tests like MIT, Florida, Princeton, Long Island and I have to admit some of the questions were pretty hard (Gibbs Free Energy, total charge of peptide, psi/phi angle).


I would go through wikipedia and Klein Organic Chemistry if you can.
2018-2019
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Thermodynamics, Chemistry Lab, Protein Modeling
MIT/State
Chem Lab: 8
Protein Modeling: 7
Thermodynamics: 14 :(

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eagerlearner102
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Re: Protein Modeling C

Postby eagerlearner102 » February 25th, 2019, 7:56 pm

For now, I am going over MIT Courseware lecture notes and transcripts.
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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