Protein Modeling C

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elephantower
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Division: C
State: AZ

Re: Protein Modeling C

Postby elephantower » March 12th, 2015, 10:04 pm

So how are you guys practicing for the onsite builds? Just like the active sites of the proteins they posted to the website?
That's what we did.
[S/N]
N/A = didn't compete

2013:
Geologic Mapping: 1, 2
Designer Genes: 3, :(
Astronomy: N/A, :(
2014:
Geologic Mapping: 1, N/A
Protein Modelling: 1, N/A
It's About Time: 1, N/A
Forensics: 9, N/A
2015:
Geologic Mapping: 1, ?
Hydrogeology: 1, ?
It's About Time: 1, ?
Forensics: 10, ?

Dhruvster
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Re: Protein Modeling C

Postby Dhruvster » March 13th, 2015, 11:24 am

So how are you guys practicing for the onsite builds? Just like the active sites of the proteins they posted to the website?
That's what we did.
Thanks! Yeah since you don't find out the build before you enter the room I suppose thats the best you can do.
Hey another quick thing, how are you guys thinking of transporting your protein out of state, like on a plane without the folding getting all mixed up.

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elephantower
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Re: Protein Modeling C

Postby elephantower » March 13th, 2015, 9:04 pm

So how are you guys practicing for the onsite builds? Just like the active sites of the proteins they posted to the website?
That's what we did.
Thanks! Yeah since you don't find out the build before you enter the room I suppose thats the best you can do.
Hey another quick thing, how are you guys thinking of transporting your protein out of state, like on a plane without the folding getting all mixed up.
Our team usually ships the materials for builds and assembles them onsite, with varying degrees of success.
[S/N]
N/A = didn't compete

2013:
Geologic Mapping: 1, 2
Designer Genes: 3, :(
Astronomy: N/A, :(
2014:
Geologic Mapping: 1, N/A
Protein Modelling: 1, N/A
It's About Time: 1, N/A
Forensics: 9, N/A
2015:
Geologic Mapping: 1, ?
Hydrogeology: 1, ?
It's About Time: 1, ?
Forensics: 10, ?

bernard
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Re: Protein Modeling C

Postby bernard » March 14th, 2015, 12:32 am

So how are you guys practicing for the onsite builds? Just like the active sites of the proteins they posted to the website?
That's what we did.
Thanks! Yeah since you don't find out the build before you enter the room I suppose thats the best you can do.
Hey another quick thing, how are you guys thinking of transporting your protein out of state, like on a plane without the folding getting all mixed up.
I'm not experienced with how well things survive shipping, but could you just put it in a box? Of course you would need some adjustments because of how malleable the minitoobers are, but hopefully they are minimal.
"One of the ways that I believe people express their appreciation to the rest of humanity is to make something wonderful and put it out there."

annaphase
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Re: Protein Modeling C

Postby annaphase » March 15th, 2015, 3:17 pm

Thanks! Yeah since you don't find out the build before you enter the room I suppose thats the best you can do.
Hey another quick thing, how are you guys thinking of transporting your protein out of state, like on a plane without the folding getting all mixed up.
I'm not experienced with how well things survive shipping, but could you just put it in a box? Of course you would need some adjustments because of how malleable the minitoobers are, but hopefully they are minimal.
I know it's not quite the same, but for states we had a seven hour drive and we were required to keep stuff under the coach bus so to protect my baby (the protein haha) I put it in a large wooden crate. For some context, my protein itself was suspended within a frame so the crate around it just ensured that it didn't get banged around by other stuff. We also carefully marked the crate with "THIS SIDE UP" and "PROTEIN MODELING-PLEASE DO NOT TOUCH" and it did survive so...yeah
"What are the squiggly things for?"~Protein Modeling
"150 degrees Celsius? Either this graph is wrong, or the only place this enzyme is active is in hell." ~Cell Bio

Dhruvster
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Re: Protein Modeling C

Postby Dhruvster » March 17th, 2015, 2:22 pm

Yeah my idea was to just put it in some kind of crate to hold it all together and make sure nothing gets ruined. Lol I'm relieved to see others going crazy too with keeping the protein safe.

So I realize the DNA is an obvious addition which everyone is going to have. Its just that the proctors have always given me negative comments about how my pitch and amplitude is off, and how my placement could be better. Has anyone found a solid material that works well when building the DNA or knows how to calculate a pitch and amplitude in sync with the 2cm to 1 amino acids size?

annaphase
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Re: Protein Modeling C

Postby annaphase » March 17th, 2015, 8:09 pm

Yeah my idea was to just put it in some kind of crate to hold it all together and make sure nothing gets ruined. Lol I'm relieved to see others going crazy too with keeping the protein safe.

So I realize the DNA is an obvious addition which everyone is going to have. Its just that the proctors have always given me negative comments about how my pitch and amplitude is off, and how my placement could be better. Has anyone found a solid material that works well when building the DNA or knows how to calculate a pitch and amplitude in sync with the 2cm to 1 amino acids size?
For your second question, a lot of jMol files include DNA in them, and you can adapt a scale from there, assuming the protein is being built at the same scale. I know there are acailable files of FokI bound to DNA so that souldn't be extremly difficult to locate.
As for the material, I posted earlier but what I finally settled on was actually leftover minitoobers from past competion years held together with jewlery wire bent in the general pentagoal/hexagonal shape of the bound DNA bases that represent FokI's binding sequence, and that stood up to trial and tribulation and I got a judge's complement on its accuracy (I just didn't know the tiebreaker quesiton pigeon I was so close :evil: :oops: :x :( but good luck to you!
"What are the squiggly things for?"~Protein Modeling
"150 degrees Celsius? Either this graph is wrong, or the only place this enzyme is active is in hell." ~Cell Bio

SAmoyo
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Re: Protein Modeling C

Postby SAmoyo » March 20th, 2015, 4:58 am

Are questions about the zinc finger protein going to be asked at the state competition level, or is it going to be just on the TALE nuclease proteins?

Sushies
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Re: Protein Modeling C

Postby Sushies » March 20th, 2015, 8:20 am

Yeah my idea was to just put it in some kind of crate to hold it all together and make sure nothing gets ruined. Lol I'm relieved to see others going crazy too with keeping the protein safe.

So I realize the DNA is an obvious addition which everyone is going to have. Its just that the proctors have always given me negative comments about how my pitch and amplitude is off, and how my placement could be better. Has anyone found a solid material that works well when building the DNA or knows how to calculate a pitch and amplitude in sync with the 2cm to 1 amino acids size?
For your second question, a lot of jMol files include DNA in them, and you can adapt a scale from there, assuming the protein is being built at the same scale. I know there are acailable files of FokI bound to DNA so that souldn't be extremly difficult to locate.
As for the material, I posted earlier but what I finally settled on was actually leftover minitoobers from past competion years held together with jewlery wire bent in the general pentagoal/hexagonal shape of the bound DNA bases that represent FokI's binding sequence, and that stood up to trial and tribulation and I got a judge's complement on its accuracy (I just didn't know the tiebreaker quesiton butterfly I was so close :evil: :oops: :x :( but good luck to you!
Regarding your last sentence, you mention the specific sequence bound by FokI's binding domain. It was my understanding that we modeled the catalytic domain and the portion of DNA cleaved by our model is nonspecific. Did you additionally model the DNA-recognition domain?
2014: Circuit Lab, Designer Genes, MagLev. Trial: Environmental Chemistry
2015: Astronomy, Bridges, Protein Modeling, Chemistry Lab.

Giant Mole Squad
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Re: Protein Modeling C

Postby Giant Mole Squad » March 21st, 2015, 9:02 am

Does anyone know if the website provided on the event description for the visualization environment (MSOE CBM) is what will be used at the state competitions? Or is Jmol completely different? Our regionals used some downloaded software that I don't think was correct...


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