Protein Modeling C

Uber
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Re: Protein Modeling C

Postby Uber » January 30th, 2016, 8:55 pm

I noticed the same issue... I glued on one of the endcaps to fix this for the prebuild. I am wondering though - I saw this issue on the practice onsite build and my invitational build today. Is it science olympiad's fault, or is the notation different than we thought?
Partner found the same thing. Alpha carbon is definitely the middle of the 2cm, not the edges. They probably just derped and subtracted without adding one.
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Noel
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Re: Protein Modeling C

Postby Noel » January 31st, 2016, 8:29 am

Hey Guys,

Is anyone else having trouble getting the Pre-Build protein model from the pre-build environment. This year we have to build amino acids 93-261 of chain A of the Sepiapterin Reductase, so when I type "restrict 93-261 and sidechain=a" just like the tutorial says, the protein disappears completely.

Any thoughts?

Also, if we're going to build a support stand for our protein, does the support stand have and dimensional restrictions?

Thanks
Try typing...
backbone .7
cartoon off
restrict 93-261 and chain = A

Also, there are no restrictions on the dimensions of the support stand but you should keep them in mind for the convenience of packing and transportation.
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Noel
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Re: Protein Modeling C

Postby Noel » January 31st, 2016, 8:47 am

We have purchased the 3 D molecular design’s 2015-2016 Science Olympiad Protein Modeling Event Kit (pre- build Kit). The site says it is for 168 amino acids but this year’s protein needs 169 and we found the mini-toobers are short by 2 centimeters. Has anyone else ordered the kit and had the same problem? If so, how did you add the two centimeters?
A team from our state noticed the same issue. You can glue on your red and blue caps so they are only attached to 1 cm of the toober. Assuming that the caps are 2 cm each this will add 2 cm total to your protein.
There is no problem with the kit. The scale is 2 cm per amino acid, which really means that there are 2 cm between each amino acid. If you go on Jmol and color one amino acid you will see that the color covers one bend and halfway to the bend on either side. So each amino acid is represented by the turn - not the connection. The backbone structure connects amino acids linearly, rather than creating smooth turns like in the cartoon visualization. So, getting back to the kit, you need 2 cm between each amino acid. Say the protein was from amino acids 5 to 9 (hypothetically), that would mean your structure would be as follows with the dashes representing the 2 cm of tuber you need.
5 - 6 - 7 - 8 - 9
That's four dashes, 4 * 2 = 8 cm of tuber. More simply, (9-5) * 2 = 8. In the case of this years protein, we have to build amino acids 93 - 261. So, (261- 93) * 2 = (168) * 2 = 336 cm of tuber, which is what the kit provides.
I know it's confusing because there are 169 amino acids but you have to understand that the first and last amino acids are at the ends of the tuber. And when you restrict the amino acids visualized in Jmol, the program will eliminate one cm of backbone connecting to amino acid 92 and one cm of backbone connecting to amino acid 264, which is why the kit provides 2 cm less tuber than you might expect.
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Re: Protein Modeling C

Postby [mango] » February 2nd, 2016, 8:18 pm

I could not find this directly specified anywhere. Does the onsite protein model require us to add creative additions?

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Re: Protein Modeling C

Postby Uber » February 2nd, 2016, 8:35 pm

I could not find this directly specified anywhere. Does the onsite protein model require us to add creative additions?
Nope.
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Re: Protein Modeling C

Postby [mango] » February 12th, 2016, 5:44 pm

I have another question: Does the regional test typically cover the invitational protein as well?

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Re: Protein Modeling C

Postby ElementalClockwork » February 12th, 2016, 7:21 pm

I have another question: Does the regional test typically cover the invitational protein as well?
From what I remember from doing the event last year, nope. Pretty sure the regional test only covers the regional on-site model & the prebuild.

Also another quick question, is it a good idea to indicate the binding sites for BH4 on the model itself? Do people typically do this? I figured I'd just stick labels where BH4 binds to the enzyme.
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Re: Protein Modeling C

Postby jkatz16 » February 14th, 2016, 6:55 am

Hey guys, I am having trouble restricting the dopamine transport on-site model on jmol (pdb file is 4m48.pdb.). When I go to restrict a random length (example: restrict 100-164) I end up getting multiple pieces that are not attached to each other. Does anyone know why this might be the case? What do I have to do to only end up with one piece?

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Re: Protein Modeling C

Postby Fluorine » February 16th, 2016, 2:30 pm

This event forum is pretty inactive but going to ask anyway.

So our team at the past several competitions has been getting perfect or near perfect on both the prebuild and the onsite build. But the test portion of this event we consistently do sub-par on. Does anyone have any tips on doing better on the exam for this event? Right now our plan is to read a lot more research papers and add more information to our reference sheet. Any help is much appreciated as our teams is starting to feel a little stuck.

Also feel free to PM me if you want

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Re: Protein Modeling C

Postby inwhite » February 16th, 2016, 2:43 pm

This event forum is pretty inactive but going to ask anyway.

So our team at the past several competitions has been getting perfect or near perfect on both the prebuild and the onsite build. But the test portion of this event we consistently do sub-par on. Does anyone have any tips on doing better on the exam for this event? Right now our plan is to read a lot more research papers and add more information to our reference sheet. Any help is much appreciated as our teams is starting to feel a little stuck.

Also feel free to PM me if you want
I've been having the same problem. We constantly see perfect scores on our models and then, like, 50% for our test. We're currently doing the same thing as you suggested. Make sure you have the obvious (a codon table, info about invitational, regional, state, and national proteins, amino acid table, structures of the neurotransmitters, etc.) if you don't already have it, because those can cost you a ton of points.

Check the wiki for some info as well, if you haven't already.
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