Protein Modeling C

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huppada
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Re: Protein Modeling C

Post by huppada » January 22nd, 2020, 6:34 pm

itsDerk wrote:
January 21st, 2020, 6:34 pm
svph300 wrote:
January 21st, 2020, 11:47 am
huppada wrote:
January 21st, 2020, 4:02 am

In that case, (for those who are going) is everyone sticking to the BE4 plasmid for the MIT Invitational this weekend?

Also, I’ve submitted requests for rules clarifications, asking whether BE4 is the correct plasmid we’re supposed to model and if we’re supposed to model the expression plasmid separately to the cytidine deaminase protein.
From my interpretation, the competitors are expected to create a theoretical model of APOBEC3A (which is the prebuild for this year and also different from APOBEC-1) within the larger fusion protein of the BE4 expression plasmid. I think that competitors need to build a schematic representation of APOBEC3A and how it could theoretically fit within the BE4 expression plasmid, since it's actually APOBEC-1 that interacts with the BE4 expression plasmid. Also, I've read research articles to make sure that there's no known relationship between APOBEC3A and BE4 expression plasmid and I haven't seen any relationships whatsoever between these two. In other words, you would have two models: a model of APOBEC3A (prebuild) and a theoretical model of BE4 expression plasmid (add-on; what competitors need to create). Also, don't forget to consider other regions of the fusion protein and their connections to each other as well (this is explicitly stated in the rules). I hope this interpretation made sense.

I agree that there seems to be a disconnect between MSOE and SOINC. As I mentioned, I haven't read any research papers discussing the relationship of APOBEC3A with the BE4 expression plasmid. From the addgene website and the papers I've read, it's APOBEC-1 that has a direct relationship with the BE4 expression plasmid. However, I have read papers about APOBEC3A and the BE3 plasmid, and I think it would make more sense for competitors to make a model of the BE3 instead of the BE4 expression plasmid.

TL;DR: Make a schematic representation of the relationship between APOBEC3A, BE4 expression plasmid, and other regions of the fusion protein in the correct linear order. Possible disconnect between MSOE and SOINC regarding the rules.
This is what I've seen thru the available literature as well. It's just interesting that even the original 5td5 pdb file didn't match up with BE4 in the first version of the rules. Thanks for the feedback everyone. Hopefully there will be some rule clarification or response soon, but for MIT I guess we're just gonna have to run with it.

Good luck to all those going to MIT! It'll be a good one.
Protein Modeling
Rules Clarification (4.b.iii.3): The National level of competition requires that teams include "schematic representations of the other regions of the fusion protein and their connections to each other." We will score the event by awarding the same credit for all models, regardless of completeness, that have at least some representation of the other regions of the fusion protein. Models should provide enough evidence to substantiate that competitors know of and have depicted the other regions of the fusion protein, their connections to each other, and that these regions are depicted in the correct linear order.

^^^I found this on MIT's SciOly website. It seems like they will give credit as long as we make an attempt. Hope to see everyone at MIT this Saturday!
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Re: Protein Modeling C

Post by MacintoshJosh » January 31st, 2020, 5:21 pm

Given a protein in Jmol, and without using any external resources - just Jmol, how would one find the method used to solve the structure of the protein as well as the resolution of the protein? I was asked these questions on an invitational test, and I really can't seem to figure out how you could find them.
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Re: Protein Modeling C

Post by CookiePie1 » February 1st, 2020, 7:12 am

MacintoshJosh wrote:
January 31st, 2020, 5:21 pm
Given a protein in Jmol, and without using any external resources - just Jmol, how would one find the method used to solve the structure of the protein as well as the resolution of the protein? I was asked these questions on an invitational test, and I really can't seem to figure out how you could find them.
if you open the text file of the pdb file, it says the method next to 'EXPDTA' near the beginning of the file.
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Re: Protein Modeling C

Post by MacintoshJosh » February 1st, 2020, 11:11 am

CookiePie1 wrote:
February 1st, 2020, 7:12 am
MacintoshJosh wrote:
January 31st, 2020, 5:21 pm
Given a protein in Jmol, and without using any external resources - just Jmol, how would one find the method used to solve the structure of the protein as well as the resolution of the protein? I was asked these questions on an invitational test, and I really can't seem to figure out how you could find them.
if you open the text file of the pdb file, it says the method next to 'EXPDTA' near the beginning of the file.
I see it, thanks so much!
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Re: Protein Modeling C

Post by svph300 » February 1st, 2020, 6:28 pm

Hi everyone! I have linked Protein Modeling Exams that I have written this season in this post. I will also release the 2020 UT Austin Regional Competition Exam I wrote after the competition day. Feel free to reach out to me with any comments or questions about my exams or this event in general. I hope this serves to be a useful and helpful resource to everyone, and good luck!

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2019 Cornell Invitational
2019 Northview Invitational
2019 Orlando Science School Invitational
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Re: Protein Modeling C

Post by CookiePie1 » February 1st, 2020, 7:30 pm

svph300 wrote:
February 1st, 2020, 6:28 pm
Hi everyone! I have linked Protein Modeling Exams that I have written this season in this post. I will also release the 2020 UT Austin Regional Competition Exam I wrote after the competition day. Feel free to reach out to me with any comments or questions about my exams or this event in general. I hope this serves to be a useful and helpful resource to everyone, and good luck!

2019 UT Austin Invitational
2019 Cornell Invitational
2019 Northview Invitational
2019 Orlando Science School Invitational
2020 Plymouth Invitational
OMG thank you sooo much
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Re: Protein Modeling C

Post by Mr.Epithelium » February 1st, 2020, 9:48 pm

CookiePie1 wrote:
February 1st, 2020, 7:30 pm
svph300 wrote:
February 1st, 2020, 6:28 pm
Hi everyone! I have linked Protein Modeling Exams that I have written this season in this post. I will also release the 2020 UT Austin Regional Competition Exam I wrote after the competition day. Feel free to reach out to me with any comments or questions about my exams or this event in general. I hope this serves to be a useful and helpful resource to everyone, and good luck!

2019 UT Austin Invitational
2019 Cornell Invitational
2019 Northview Invitational
2019 Orlando Science School Invitational
2020 Plymouth Invitational
OMG thank you sooo much
Yes! love to see what these tests have to say about CRISPR lol
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Re: Protein Modeling C

Post by svph300 » February 3rd, 2020, 8:48 am

Mr.Epithelium wrote:
February 1st, 2020, 9:48 pm
CookiePie1 wrote:
February 1st, 2020, 7:30 pm
svph300 wrote:
February 1st, 2020, 6:28 pm
Hi everyone! I have linked Protein Modeling Exams that I have written this season in this post. I will also release the 2020 UT Austin Regional Competition Exam I wrote after the competition day. Feel free to reach out to me with any comments or questions about my exams or this event in general. I hope this serves to be a useful and helpful resource to everyone, and good luck!

2019 UT Austin Invitational
2019 Cornell Invitational
2019 Northview Invitational
2019 Orlando Science School Invitational
2020 Plymouth Invitational
OMG thank you sooo much
Yes! love to see what these tests have to say about CRISPR lol
You're welcome! I hope they're challenging and useful learning resources.

Update: These exams (along with the keys and answer sheets) are now uploaded on the Test Exchange. Reach out if you have any questions!
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Re: Protein Modeling C

Post by Arbiter604 » February 4th, 2020, 9:09 pm

CookiePie1 wrote:
February 1st, 2020, 7:12 am
MacintoshJosh wrote:
January 31st, 2020, 5:21 pm
Given a protein in Jmol, and without using any external resources - just Jmol, how would one find the method used to solve the structure of the protein as well as the resolution of the protein? I was asked these questions on an invitational test, and I really can't seem to figure out how you could find them.
if you open the text file of the pdb file, it says the method next to 'EXPDTA' near the beginning of the file.
How do you open the text file of the pdb file in Jmol?
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Re: Protein Modeling C

Post by CookiePie1 » February 5th, 2020, 8:53 am

Arbiter604 wrote:
February 4th, 2020, 9:09 pm
CookiePie1 wrote:
February 1st, 2020, 7:12 am
MacintoshJosh wrote:
January 31st, 2020, 5:21 pm
Given a protein in Jmol, and without using any external resources - just Jmol, how would one find the method used to solve the structure of the protein as well as the resolution of the protein? I was asked these questions on an invitational test, and I really can't seem to figure out how you could find them.
if you open the text file of the pdb file, it says the method next to 'EXPDTA' near the beginning of the file.
How do you open the text file of the pdb file in Jmol?
use "show file"
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2020 Events: Protein Modeling, Ping Pong Parachute, Wright Stuff, Sounds of Music

Reality is merely an illusion, albeit a very persistent one.
-Albert Einstein

Check out my userpage!

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