Protein Modeling C

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Re: Protein Modeling C

Postby meierfra » November 18th, 2018, 12:00 pm

rhkoulen wrote:
Limke wrote:
rhkoulen wrote:How can you convert the mess of 4un3 to something that doesn't give me a stroke when you look at it?

Any links to tutorials would be nice too thanks.


The MSOE website has a bunch of tutorials on how to use Jmol and restrict domains (removing all the residues you don't need, showing certain sidechains, restricting to just the backbone (2ndary structure)

http://cbm.msoe.edu/scienceOlympiad/participant3.php

Scroll down on that page and they should have links under their Advanced Jmol training guide, which I found particularly helpful!


Thank you so much!


You realize that for the Pre-build there's a Rules Clarification and we're supposed to do 5vw1, right?

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Re: Protein Modeling C

Postby rhkoulen » November 18th, 2018, 4:11 pm

Dude, I like, uhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh just did the whole dam thang for 4un3 so like


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Re: Protein Modeling C

Postby KSSOISLIT » November 19th, 2018, 2:15 pm

Does anyone here know what specific criteria judges use to grade the pre-build? I.e. a rubric? I understand how they grade for basic structure stuff, but how do they designate different point values for the creative additions? Thanks...
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Re: Protein Modeling C

Postby pikachu4919 » November 19th, 2018, 2:38 pm

KSSOISLIT wrote:Does anyone here know what specific criteria judges use to grade the pre-build? I.e. a rubric? I understand how they grade for basic structure stuff, but how do they designate different point values for the creative additions? Thanks...


There is a rubric, but I believe it's usually only given to event supervisors.
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Re: Protein Modeling C

Postby labgirl » November 19th, 2018, 3:47 pm

Hey guys!

Just a clarification (because it's not specified on the rules) the residues 1-85 refers to those on the B chain, correct? It's the only chain actually labeled "Anti-CRISPR protein," but I'd like confirmation before I show up to competition with the wrong chain. XP

Also, does anyone have any tips for finding what "functionally relevant features" to note on the model? I did this as a trial event last year, and trying to figure out what to mark was the thing my partner and I struggled with the most.

Thanks! :)

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Re: Protein Modeling C

Postby pikachu4919 » November 19th, 2018, 4:36 pm

labgirl wrote:Hey guys!

Just a clarification (because it's not specified on the rules) the residues 1-85 refers to those on the B chain, correct? It's the only chain actually labeled "Anti-CRISPR protein," but I'd like confirmation before I show up to competition with the wrong chain. XP

Also, does anyone have any tips for finding what "functionally relevant features" to note on the model? I did this as a trial event last year, and trying to figure out what to mark was the thing my partner and I struggled with the most.

Thanks! :)


To the first question, I believe so. After playing around with it in the JSmol on CBM's website, it appears that the 5vw1.pdb file contains an A and a B chain, however, after manipulating a handful of things in the environment, it appears that the B chain seems to be 85 residues long (not counting residue 0, which exists in this pdb file) and is completely detached from the A chain (which is many more amino acids long yet still has a 1-85 as well). However, the provided JSmol design environment on the official website for protein modeling does say B chain in its prebuild visualization environment, which is why you could reasonably suspect that the prebuild is that way. If you really, really want to make sure, you could submit a FAQ or clarification to the National Committee here if you feel like it.

In terms of the bonus "functionally relevant features" part, my best recommendation is to read the paper that the protein is based off of to determine those. The paper will give you plenty of ideas by mentioning several different very crucial amino acids, ligands, or any other things critical to the protein function. Then it's up to you to decide which ones you would want to portray, if any, and how you want to do that.
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Re: Protein Modeling C

Postby EastStroudsburg13 » November 20th, 2018, 6:37 am

pikachu4919 wrote:
KSSOISLIT wrote:Does anyone here know what specific criteria judges use to grade the pre-build? I.e. a rubric? I understand how they grade for basic structure stuff, but how do they designate different point values for the creative additions? Thanks...


There is a rubric, but I believe it's usually only given to event supervisors.

Also, from what I recall, the rubric differs depending on the level of competition. The state and national rubrics had progressively higher standards to earn points, especially for the additions.
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Re: Protein Modeling C

Postby platypusomelette » November 20th, 2018, 7:18 am

EastStroudsburg13 wrote:
pikachu4919 wrote:
KSSOISLIT wrote:Does anyone here know what specific criteria judges use to grade the pre-build? I.e. a rubric? I understand how they grade for basic structure stuff, but how do they designate different point values for the creative additions? Thanks...


There is a rubric, but I believe it's usually only given to event supervisors.

Also, from what I recall, the rubric differs depending on the level of competition. The state and national rubrics had progressively higher standards to earn points, especially for the additions.


Wait do you know where to find sample rubrics?
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Re: Protein Modeling C

Postby EastStroudsburg13 » November 20th, 2018, 7:29 am

platypusomelette wrote:
EastStroudsburg13 wrote:
pikachu4919 wrote:
There is a rubric, but I believe it's usually only given to event supervisors.

Also, from what I recall, the rubric differs depending on the level of competition. The state and national rubrics had progressively higher standards to earn points, especially for the additions.


Wait do you know where to find sample rubrics?

I don't think there is any central repository, but the wiki has two examples from past national tournaments linked to in its description of the on-site model.
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Re: Protein Modeling C

Postby aaaaaa » November 21st, 2018, 2:44 pm

Wait how do we figure out the amino acid sequence of the Anti-Crispr

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Re: Protein Modeling C

Postby ericlepanda » November 21st, 2018, 3:45 pm

aaaaaa wrote:Wait how do we figure out the amino acid sequence of the Anti-Crispr

you can find the sequences for both the anti-crispr and the cas-9 on rcsb
http://www.rcsb.org/pdb/explore/remedia ... ureId=5VW1
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Re: Protein Modeling C

Postby PeptoBismol » November 22nd, 2018, 12:48 pm

With 5vw1, I restricted it to the b chain only and found that, when I restricted it to 1-60 through 1-85 nothing happened, but when I restricted it to 1-59, some of the chain was removed, which makes me believe the b chain is 60 residues long. But I know it is at least 85 long, so how does this work out? Am I doing something wrong, or does the build contain both a and b?

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Re: Protein Modeling C

Postby JoeyC » November 22nd, 2018, 1:09 pm

restrict 1-85
restrict :b
If the chain does not have 3 Alpha Helices and 3 Beta Pleated Sheets, your program is recognizing the wrong chain.
It should look as such: https://drive.google.com/file/d/1UQgeeSXoNnIR7ZOjLpnYPizFRMJlR7bK/view?usp=sharing
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Re: Protein Modeling C

Postby greenMountainCoffee » November 25th, 2018, 3:29 pm

Hi,
This may be a stupid question, but on the JSMOL thing, it says the protein we should build is 84 residues long. Does that mean we should include residue #1 and include residue #84?

Sorry this was worded weirdly too

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Re: Protein Modeling C

Postby Limke » November 25th, 2018, 3:31 pm

greenMountainCoffee wrote:Hi,
This may be a stupid question, but on the JSMOL thing, it says the protein we should build is 84 residues long. Does that mean we should include residue #1 and include residue #84?

Sorry this was worded weirdly too


Yes, include residue 1 and 85*.
Also, just a clarification, the rules say to build residues 1-85.
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