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, Wright Stuff

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

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 » March 17th, 2019, 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 » March 17th, 2019, 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, Wright Stuff

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

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Re: Protein Modeling C

Postby Birdmusic » March 28th, 2019, 5:27 pm

Help, we have a bit more until a week before states, and turns out I need to sub for this event and learn some thoery (I don't have to help w the actual modelling or whatever that parts about). What would you guys recommend? They linked me to a video, their notes, and khanacademy. Is there anything I need to know about this event?
I like birds.

2018 Results
R/S
Crime Busters: 1/2
Disease Detectives: 1/5
Hovercraft (both builds failed, rip): 11/9

2019 Results
GGSO/R/S
Disease Detectives: 6/3/10
Circuit lab:11/4/-
Sounds:3/2/1
Protein: -/-/6

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JoeyC
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Re: Protein Modeling C

Postby JoeyC » March 28th, 2019, 5:32 pm

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5595222/
is a pretty good source. It's a bit information rich
Knowing a ton about the amino acids and how they influence protein structure (as well as their groups ex: aliphatic group/helix breakers) is very important. Get a chart of those (groups) on your notes.
AP Chem/Bio knowledge is important (in the areas that relate to this).
And finally the prebuild and onsite will be hard if you don't know how to use the program. Watch some tutorials, and this :https://chemapps.stolaf.edu/jmol/docs/?ver=14.22#colormodelobject can be useful (but only once you've watched some tutorials as its mainly just a documentation of commands).
Ohayo!
Past (Main) Events
Dynamic Planet Fast Facts, Thermodynamics, Green Generation

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

Birdmusic
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Re: Protein Modeling C

Postby Birdmusic » March 28th, 2019, 5:32 pm

JoeyC wrote:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5595222/
is a pretty good source. It's a bit information rich
Knowing a ton about the amino acids and how they influence protein structure (as well as their groups ex: aliphatic group/helix breakers) is very important. Get a chart of those (groups) on your notes.
AP Chem/Bio knowledge is important (in the areas that relate to this).
And finally the prebuild and onsite will be hard if you don't know how to use the program. Watch some tutorials, and this :https://chemapps.stolaf.edu/jmol/docs/?ver=14.22#colormodelobject can be useful (but only once you've watched some tutorials as its mainly just a documentation of commands).

Thank you!
I like birds.

2018 Results
R/S
Crime Busters: 1/2
Disease Detectives: 1/5
Hovercraft (both builds failed, rip): 11/9

2019 Results
GGSO/R/S
Disease Detectives: 6/3/10
Circuit lab:11/4/-
Sounds:3/2/1
Protein: -/-/6

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CookiePie1
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Re: Protein Modeling C

Postby CookiePie1 » March 28th, 2019, 5:34 pm

Birdmusic wrote:
JoeyC wrote:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5595222/
is a pretty good source. It's a bit information rich
Knowing a ton about the amino acids and how they influence protein structure (as well as their groups ex: aliphatic group/helix breakers) is very important. Get a chart of those (groups) on your notes.
AP Chem/Bio knowledge is important (in the areas that relate to this).
And finally the prebuild and onsite will be hard if you don't know how to use the program. Watch some tutorials, and this :https://chemapps.stolaf.edu/jmol/docs/?ver=14.22#colormodelobject can be useful (but only once you've watched some tutorials as its mainly just a documentation of commands).

Thank you!


I also reccomend checking out as much as you can here: http://cbm.msoe.edu/scienceOlympiad/
It has a lot of information, and is great especially since you're just starting.
South Brunswick High School '22
2019 Events: Thermodynamics, Protein Modeling, Mission Possible, Wright Stuff

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

Birdmusic
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Re: Protein Modeling C

Postby Birdmusic » March 28th, 2019, 8:55 pm

CookiePie1 wrote:I also reccomend checking out as much as you can here: http://cbm.msoe.edu/scienceOlympiad/
It has a lot of information, and is great especially since you're just starting.

Thanks!
I like birds.

2018 Results
R/S
Crime Busters: 1/2
Disease Detectives: 1/5
Hovercraft (both builds failed, rip): 11/9

2019 Results
GGSO/R/S
Disease Detectives: 6/3/10
Circuit lab:11/4/-
Sounds:3/2/1
Protein: -/-/6

Greendown
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Re: Protein Modeling C

Postby Greendown » April 2nd, 2019, 6:13 pm

huppada wrote:
CookiePie1 wrote:
huppada wrote: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 :)

The entire time I thought it meant to make the three helices form a triangle so that’s what we made the model look like at every competition.


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