Protein Modeling C

adaline16
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Re: Protein Modeling C

Postby adaline16 » March 15th, 2019, 5:20 am

Hi Everyone,
Every time I have submitted my pre-built, I have been docked points because my model doesn't "look like a triangle" and all secondary structures aren't compact in placement." Does anyone have any idea what the proctor could possibly mean, especially with the triangular shape? Thanks.

huppada
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Re: Protein Modeling C

Postby huppada » March 15th, 2019, 9:07 am

adaline16 wrote:Hi Everyone,
Every time I have submitted my pre-built, I have been docked points because my model doesn't "look like a triangle" and all secondary structures aren't compact in placement." Does anyone have any idea what the proctor could possibly mean, especially with the triangular shape? Thanks.

I think the overall structure should somewhat make a triangular shape when looking at it from the side. This kind of makes sense if you imagine the beta sheet forming the base of the triangle, and the second and third alpha helices crossing over in a way to represent the other sides of the triangle.
Orlando Science Schools '20
2019 Events: Anatomy & Physiology, Disease Detectives, Protein Modeling

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CookiePie1
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Re: Protein Modeling C

Postby CookiePie1 » March 15th, 2019, 12:29 pm

huppada wrote:
adaline16 wrote:Hi Everyone,
Every time I have submitted my pre-built, I have been docked points because my model doesn't "look like a triangle" and all secondary structures aren't compact in placement." Does anyone have any idea what the proctor could possibly mean, especially with the triangular shape? Thanks.

I think the overall structure should somewhat make a triangular shape when looking at it from the side. This kind of makes sense if you imagine the beta sheet forming the base of the triangle, and the second and third alpha helices crossing over in a way to represent the other sides of the triangle.


Is this what you mean? I know that I spent a lot of time trying to get this right.
Image
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?

huppada
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Re: Protein Modeling C

Postby huppada » March 16th, 2019, 1:37 pm

CookiePie1 wrote:
huppada wrote:
adaline16 wrote:Hi Everyone,
Every time I have submitted my pre-built, I have been docked points because my model doesn't "look like a triangle" and all secondary structures aren't compact in placement." Does anyone have any idea what the proctor could possibly mean, especially with the triangular shape? Thanks.

I think the overall structure should somewhat make a triangular shape when looking at it from the side. This kind of makes sense if you imagine the beta sheet forming the base of the triangle, and the second and third alpha helices crossing over in a way to represent the other sides of the triangle.


Is this what you mean? I know that I spent a lot of time trying to get this right.
Image

Ya I think the triangle shape would be better seen if you orient the protein so the yellow beta sheet is at the bottom and the helices are on the top half.
Also, side note, reducing the thickness of the backbone may make it easier on the eyes :)
Orlando Science Schools '20
2019 Events: Anatomy & Physiology, Disease Detectives, Protein Modeling

TpRelic
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Re: Protein Modeling C

Postby TpRelic » Yesterday, 2:58 pm

Hi, and thank you beforehand.
First, Is it worth writing down "AcrIIA4 is represented with yellow tubing" or ordering of the secondary structures on the notecard?
Second, I've accepted that my craftsmanship is rather lackluster,
Image - https://imgur.com/h1z8L6g
Is it okay I forgo points on the structure?
(I removed everything else from the model... it looks so bare as just tubing...)

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Re: Protein Modeling C

Postby CookiePie1 » Yesterday, 3:17 pm

TpRelic wrote:Hi, and thank you beforehand.
First, Is it worth writing down "AcrIIA4 is represented with yellow tubing" or ordering of the secondary structures on the notecard?
Second, I've accepted that my craftsmanship is rather lackluster,
Image - https://imgur.com/h1z8L6g
Is it okay I forgo points on the structure?
(I removed everything else from the model... it looks so bare as just tubing...)


1. Writing the color of AcrIIA4 is good only if you have other structures in your model. Order of secondary structures is based on the model, not what you write.
2. Most of your points will be earned from having a structure as accurate as possible, which is more important than creative additions. As a general rule of thumb, if you know you'll lose points, don't just leave it like that. Try to make it the best you can.
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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