Protein Modeling C

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eagerlearner102
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Re: Protein Modeling C

Postby eagerlearner102 » February 6th, 2019, 6:29 pm

Also, the research paper was talking about the significance of asp14. I am kind of confused by what they meant. Do they mean that occupying the phosphate lock loop prevents guide RNA from being formed (target heteroduplex)? I am confused.
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Re: Protein Modeling C

Postby shivanirao21 » February 7th, 2019, 3:53 pm

thoughts on adding the sgRNA to the model? for regionals, my partner and i built just the AcrIIA4 with significant side chains... and i think adding more would have earned us more points. we want to add on for states. would adding the sgRNA be too much??
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Re: Protein Modeling C

Postby CookiePie1 » February 7th, 2019, 4:18 pm

shivanirao21 wrote:thoughts on adding the sgRNA to the model? for regionals, my partner and i built just the AcrIIA4 with significant side chains... and i think adding more would have earned us more points. we want to add on for states. would adding the sgRNA be too much??


I don't think it's too much; rather it's important to the Cas9 protein, but AcrIIA4 doesn't directly affect the sgRNA. Therefore, you might be better off adding some of the parts that AcrIIA4 directly interacts with.
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Re: Protein Modeling C

Postby Unome » February 8th, 2019, 1:37 pm

Rules clarification as of today: the points distribution is 20% pre-build, 40% onsite build, and 40% test. This might be one of the latest rules clarification ever issued, and it's a rather major one too.

https://www.soinc.org/events/rules-clarifications
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Re: Protein Modeling C

Postby EastStroudsburg13 » February 8th, 2019, 4:52 pm

Unome wrote:Rules clarification as of today: the points distribution is 20% pre-build, 40% onsite build, and 40% test. This might be one of the latest rules clarification ever issued, and it's a rather major one too.

https://www.soinc.org/events/rules-clarifications

I'm really curious about the reasoning behind it. For the rules clarification to happen this late, and for it to be one that has such a big impact, there has to be some major reason they felt like they had to do it.
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Re: Protein Modeling C

Postby CookiePie1 » February 8th, 2019, 6:17 pm

EastStroudsburg13 wrote:
Unome wrote:Rules clarification as of today: the points distribution is 20% pre-build, 40% onsite build, and 40% test. This might be one of the latest rules clarification ever issued, and it's a rather major one too.

https://www.soinc.org/events/rules-clarifications

I'm really curious about the reasoning behind it. For the rules clarification to happen this late, and for it to be one that has such a big impact, there has to be some major reason they felt like they had to do it.


Maybe it goes to some of the 'pay-to-win' type things. I think some schools are sinking a ton of money into it and they probably just don't want that.
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Re: Protein Modeling C

Postby primitive_polonium » February 8th, 2019, 9:06 pm

CookiePie1 wrote:
EastStroudsburg13 wrote:
Unome wrote:Rules clarification as of today: the points distribution is 20% pre-build, 40% onsite build, and 40% test. This might be one of the latest rules clarification ever issued, and it's a rather major one too.

https://www.soinc.org/events/rules-clarifications

I'm really curious about the reasoning behind it. For the rules clarification to happen this late, and for it to be one that has such a big impact, there has to be some major reason they felt like they had to do it.


Maybe it goes to some of the 'pay-to-win' type things. I think some schools are sinking a ton of money into it and they probably just don't want that.


So I'm a States supervisor for Protein Modeling. I can't say much, but my understanding is that there really isn't a lot of...safety around the prebuild rubric. It is pay-to-win.

The general gist is: if things haven't changed too much since 2015/6, I have pretty good reason to suspect that a good chunk of teams (including top teams) have the model and rubric. When I did PMod then, my Protein partner and coach got their hands on the prebuild rubric; I knew people at other schools who did the same.

The final straw was an incident of widespread distribution of the rubric. Afterwards, MSOE probably decided that it wasn't really fair to put so much value on the prebuild section and thus adjusted the score accordingly. It's a bit late to really do much else towards changing the event.
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Re: Protein Modeling C

Postby Unome » February 9th, 2019, 5:09 am

primitive_polonium wrote:
CookiePie1 wrote:
EastStroudsburg13 wrote:I'm really curious about the reasoning behind it. For the rules clarification to happen this late, and for it to be one that has such a big impact, there has to be some major reason they felt like they had to do it.


Maybe it goes to some of the 'pay-to-win' type things. I think some schools are sinking a ton of money into it and they probably just don't want that.


So I'm a States supervisor for Protein Modeling. I can't say much, but my understanding is that there really isn't a lot of...safety around the prebuild rubric. It is pay-to-win.

The general gist is: if things haven't changed too much since 2015/6, I have pretty good reason to suspect that a good chunk of teams (including top teams) have the model and rubric. When I did PMod then, my Protein partner and coach got their hands on the prebuild rubric; I knew people at other schools who did the same.

The final straw was an incident of widespread distribution of the rubric. Afterwards, MSOE probably decided that it wasn't really fair to put so much value on the prebuild section and thus adjusted the score accordingly. It's a bit late to really do much else towards changing the event.

I get the feeling that this was inevitable, considering the way the rubric is held in secret.
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Re: Protein Modeling C

Postby Person » February 9th, 2019, 9:52 am

CookiePie1 wrote:
Person wrote:Does the final alpha helix begin at Glu71, or Glu70?


In Jmol, you can just do 'color structure' and hover your mouse on where the last helix begins (I think its purple for a 3-10 helix)


I think I'm confused because looking at this, it would appear to start at Glu71, but looking at Jmol, it seems to start at Glu70. I noticed this with the other helices too - according to the sequence chain view, the first helix starts at Ile3, but the prebuild visualization environment colors it magenta starting from Asn2, etc. Should I just follow the sequence chain view from the PDB?
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Re: Protein Modeling C

Postby juakk700 » February 9th, 2019, 8:44 pm

Hello! I was looking at past rubrics from this event in the past. I was wondering if anyone knew the differences between Loops and Turns they mention? Rubric from 2010 is below.

https://scioly.org/wiki/images/2/2e/201 ... Onsite.pdf
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Re: Protein Modeling C

Postby eagerlearner102 » February 11th, 2019, 7:10 am

For the on site build, does every regional choose their own special sequence to model the protein or is it the same across the entire nation? I am asking this question because I saw the onsite build instructions from the MIT invitational.
Also, how do you really practice for the on site build considering the fact that it is now 40%?
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Re: Protein Modeling C

Postby banilmd » February 11th, 2019, 2:58 pm

eagerlearner102 wrote:For the on site build, does every regional choose their own special sequence to model the protein or is it the same across the entire nation? I am asking this question because I saw the onsite build instructions from the MIT invitational.
Also, how do you really practice for the on site build considering the fact that it is now 40%?

Me and my partner have just went along separating the protein that’s usually given to us for onsite into roughly 100 residue sections.
We just go along and practice timed building of significant structures.

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Re: Protein Modeling C

Postby platypusomelette » February 11th, 2019, 3:02 pm

juakk700 wrote:Hello! I was looking at past rubrics from this event in the past. I was wondering if anyone knew the differences between Loops and Turns they mention? Rubric from 2010 is below.

https://scioly.org/wiki/images/2/2e/201 ... Onsite.pdf

Just a theory but it looks like the turns are the parts between beta pleats specifically
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Re: Protein Modeling C

Postby primitive_polonium » February 11th, 2019, 9:37 pm

eagerlearner102 wrote:For the on site build, does every regional choose their own special sequence to model the protein or is it the same across the entire nation? I am asking this question because I saw the onsite build instructions from the MIT invitational.
Also, how do you really practice for the on site build considering the fact that it is now 40%?


Exams (written, prebuild rubric, onsite) are standardized across the board. Unless things have changed from previous years, the onsite should be the same for every regionals and every states tournament.
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Re: Protein Modeling C

Postby platypusomelette » February 12th, 2019, 9:18 am

eagerlearner102 wrote:For the on site build, does every regional choose their own special sequence to model the protein or is it the same across the entire nation? I am asking this question because I saw the onsite build instructions from the MIT invitational.
Also, how do you really practice for the on site build considering the fact that it is now 40%?

The MIT rubric was different from my regionals one though so invites are not standardized.
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2017: a&p 3rd, herp 14th
2018: a&p 1st, microbe 8th, herp 13th :/
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