Protein Modeling C

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RRapples
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Re: Protein Modeling C

Postby RRapples » January 1st, 2019, 7:43 pm

UTF-8 U+6211 U+662F wrote:
Anomaly wrote:
JoeyC wrote:That doesn't seem right https://www.soinc.org/events/rules-clarifications

Er, I meant an FAQ. sorry about that

That FAQ is for Forensics, but something similar probably applies.

I found the clarification: https://www.soinc.org/when-rules-say-ea ... ring-sheet. It is page linked to the question asked on the FAQ for Protein Modeling, so I guess it applies to both Forensics and Protein Modeling.
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UTF-8 U+6211 U+662F
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Re: Protein Modeling C

Postby UTF-8 U+6211 U+662F » January 1st, 2019, 8:02 pm

RRapples wrote:
UTF-8 U+6211 U+662F wrote:
Anomaly wrote:Er, I meant an FAQ. sorry about that

That FAQ is for Forensics, but something similar probably applies.

I found the clarification: https://www.soinc.org/when-rules-say-ea ... ring-sheet. It is page linked to the question asked on the FAQ for Protein Modeling, so I guess it applies to both Forensics and Protein Modeling.

That just means the next link on the page belongs to Protein Modeling haha

Protein Modeling has no clarifications so far

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Re: Protein Modeling C

Postby eagerlearner102 » January 2nd, 2019, 3:13 pm

When I read the 2 research papers, it mentions quite a few side chains. Does that mean I have to put every single one or some that are the most important ones?
Also, are any of you going to make a protein attached to ACRIIA4 which includes the RuvC, CTD, and TOPO domain? For me, I was considering doing the PAM duplex and the nucleic acids.
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Re: Protein Modeling C

Postby JoeyC » January 2nd, 2019, 3:27 pm

I wish you a good year then! :) :) :)
I would put about 6 side chains on there, and mark out important residues. Residues can be colored to show importance and you can you the given side chains to attach. I have all the important residues and side chains on there for a total of 7 side chains (but grouped into the functional groups they'd only count for 3 bonus features) and 14 residues highlighted (again, only counting for 2 features).Make sure to use the supports, or your model will bend wildly out of control.
Also: Don't feel bad if a proctor misgrades yours. Has happened every competition I've been to. It just be like that sometimes.
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Re: Protein Modeling C

Postby voisinet22 » January 8th, 2019, 7:41 am

I submitted an official question to the soinc site. They said it takes about a month for them to respond, hopefully that will clarify things with the rules on notes.
RRapples wrote:
UTF-8 U+6211 U+662F wrote:
Anomaly wrote:Er, I meant an FAQ. sorry about that

That FAQ is for Forensics, but something similar probably applies.

I found the clarification: https://www.soinc.org/when-rules-say-ea ... ring-sheet. It is page linked to the question asked on the FAQ for Protein Modeling, so I guess it applies to both Forensics and Protein Modeling.
..

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Re: Protein Modeling C

Postby voisinet22 » January 9th, 2019, 3:33 pm

Does anyone have advice on coloring toober sections? I have seen paint, colored tape, and markers used. I'm curious if there's a better method and whether or not to color before or after folding. Any suggestions or insights would be great.
Thanks in advance!!
-E

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Re: Protein Modeling C

Postby MitchGiff » January 10th, 2019, 1:07 pm

Hello everybody! I'm very new to this event and know very little about it, and I was wondering if there was any specific sources that really helped you to get a good grasp on this event.

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Re: Protein Modeling C

Postby CookiePie1 » January 10th, 2019, 1:59 pm

MitchGiff wrote:Hello everybody! I'm very new to this event and know very little about it, and I was wondering if there was any specific sources that really helped you to get a good grasp on this event.


you should definitely take a really good look at the rules, and also visit the CBM MSOE website here.
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Re: Protein Modeling C

Postby meierfra » January 12th, 2019, 7:10 am

Did everyone see the Rules Clarification posted yesterday? One sheet of paper per team.

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Re: Protein Modeling C

Postby voisinet22 » January 18th, 2019, 5:15 pm

freed2003 wrote:Does anyone know if for the competition they use the in-browser Jmol or the program?

In the past they have used the in-browser Jmol.

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Re: Protein Modeling C

Postby CookiePie1 » January 19th, 2019, 10:16 am

voisinet22 wrote:
freed2003 wrote:Does anyone know if for the competition they use the in-browser Jmol or the program?

In the past they have used the in-browser Jmol.


From the CBM website, it seems that the Jmol program is a last-resort for people who can't use the internet at their competitions. I think it would be a good idea to get farmiliar with both, in case you do have to use the program. They're both pretty simple and similar though, so you shouldn't have too much of a problem.
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Re: Protein Modeling C

Postby eagerlearner102 » January 20th, 2019, 10:29 am

For those that did this event in the past, do you have any idea of how many nucleotides long is the on build model? I am researching the 5f9r protein that is going to be the on build protein and on ebi.ac.uk I found some side chain to be around 30 nucleotides long.
https://www.ebi.ac.uk/pdbe/entry/pdb/5f9r/analysis
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Re: Protein Modeling C

Postby CookiePie1 » January 20th, 2019, 2:44 pm

eagerlearner102 wrote:For those that did this event in the past, do you have any idea of how many nucleotides long is the on build model? I am researching the 5f9r protein that is going to be the on build protein and on ebi.ac.uk I found some side chain to be around 30 nucleotides long.
https://www.ebi.ac.uk/pdbe/entry/pdb/5f9r/analysis


I'm not quite sure what you mean, but the onsite builds are protein chains within the regular CRISPR protein. You won't have to model any DNA. You're also not supposed to know which chains you are building onsite, so I wouldn't worry about that too much.
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Re: Protein Modeling C

Postby primitive_polonium » January 20th, 2019, 6:56 pm

eagerlearner102 wrote:For those that did this event in the past, do you have any idea of how many nucleotides long is the on build model? I am researching the 5f9r protein that is going to be the on build protein and on ebi.ac.uk I found some side chain to be around 30 nucleotides long.
https://www.ebi.ac.uk/pdbe/entry/pdb/5f9r/analysis


The onsite build will be different for every competition. You'll show up to testing, be presented with a precut toober and some amino acids, and have to build it on the spot with the help of jmol, a ruler, and a sharpie (the latter two you should bring). It'll all be protein; no DNA (although DNA is certainly within the scope of the written exam if it's an important strand).

As for length: competitions testing at the Regionals and Invitational difficulties will have onsites of ~20-30 residues. By Nationals, onsite lengths will reach up to 90. States, I surmise, will have a length in between.
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Re: Protein Modeling C

Postby greenMountainCoffee » January 21st, 2019, 4:17 pm

meierfra wrote:
greenMountainCoffee wrote:
Limke wrote:
Yes.

I measured mine out to be 85 residues.


Okay, yes (sorry this is taking so long to marinate in my brain) but the toober is only 168 cm long in the kit. 168/2 = 84....? So we must not include the actual residue of either 1 or 85 correct?


You absolutely need to include 1 and 85. Make sure the Toober is completely unwound. Sometimes if if's twisted a little, that will take up some length. Pull it all the way out, so you're sure it's at its maximum length. If it's still only 168cm, you should contact the MSOE people and ask for a replacement.

EDIT: Oops. They are sending you 168 cm and CBM gives a good explanation of why they only give you 168 cm on their Ask the CBM, question 52. https://cbm.msoe.edu/scienceOlympiad/participant2.php

Gotcha thanks!


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