Protein Modeling C

Protein Modeling C

Postby Jim_R on Sat Jul 02, 2011 10:49 pm

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Re: Protein Modeling C

Postby Phenylethylamine on Mon Aug 29, 2011 4:27 pm

Based on the way the CBM site was set up, I was under the impression that XIAP was going to be the prebuild, but apparently it's actually caspase-3.

Also, despite the fact that the Science Olympiad link in the header on the 3D Molecular Designs website still says 2010-2011, the page has already been updated for 2012. Prebuild kits will be available for order starting September 1st.
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Re: Protein Modeling C

Postby Starapollo1 on Tue Aug 30, 2011 9:33 am

So basically, we are constructing two distinct polypeptides that make up the protein as a whole?? Ionly ask cause the jmol has two seperate mini toobers... if i'm off base please help me out!
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Re: Protein Modeling C

Postby EastStroudsburg13 on Tue Aug 30, 2011 3:22 pm

What might end up happening is that we just model one of the two. I haven't looked at the jmol yet, but depending on how long each individual polypeptide is, they might just have us model one or a section of one, which is what happened last year.
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Re: Protein Modeling C

Postby butter side up on Tue Aug 30, 2011 7:13 pm

It appears that the entire protein is composed of 6 polypeptide chains, and we are building two of them. From what the website said, these are found by selecting a and selecting b.
On a related note, does anyone know how to select and isolate two separate chains at once? I can get it to show only a, and only b, but not both at once without all the other chains.
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Re: Protein Modeling C

Postby TheGenius on Tue Aug 30, 2011 7:27 pm

Try "restrict *A or *B". That should work, but I'm not able to test it currently.
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Re: Protein Modeling C

Postby butter side up on Tue Aug 30, 2011 7:48 pm

TheGenius wrote:Try "restrict *A or *B". That should work, but I'm not able to test it currently.

Thanks! That does the job very well... it should come in handy.
So I am thinking that the best way to work with the two proteins will be to suspend them both from a framework with fishing line or something, rather than propping it up with skewers in it, as we did with klf4. How do you guys support your proteins? Because the suspension looks like our best plan for now, but we are worried about transport and whatnot.
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Re: Protein Modeling C

Postby Starapollo1 on Thu Sep 01, 2011 1:32 pm

butter side up wrote:
TheGenius wrote:Try "restrict *A or *B". That should work, but I'm not able to test it currently.

Thanks! That does the job very well... it should come in handy.
So I am thinking that the best way to work with the two proteins will be to suspend them both from a framework with fishing line or something, rather than propping it up with skewers in it, as we did with klf4. How do you guys support your proteins? Because the suspension looks like our best plan for now, but we are worried about transport and whatnot.


We supsended ours last year with fishing line. Be forwarned, suspendeding can be quite frustrating lol there will be some trial and error to get it to suspend right and make sure you bring extra fish line with you to the competitions so that you can patch it up before you impound it! lol
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2012: Disease (4), Forestry (5), Microbe (-), Protein Modeling (6), Sounds of Music (7), TPS (7) overall 4th
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Re: Protein Modeling C

Postby Phenylethylamine on Thu Sep 01, 2011 9:00 pm

butter side up wrote:
TheGenius wrote:Try "restrict *A or *B". That should work, but I'm not able to test it currently.

Thanks! That does the job very well... it should come in handy.
So I am thinking that the best way to work with the two proteins will be to suspend them both from a framework with fishing line or something, rather than propping it up with skewers in it, as we did with klf4. How do you guys support your proteins? Because the suspension looks like our best plan for now, but we are worried about transport and whatnot.

I use 22-gauge jewelry wire for everything- the advantage is that it's strong enough to prop the protein up from underneath (at least, if you twist a couple strands together), but also unobtrusive enough that it doesn't obscure the protein if you use it to suspend your model. It's also a lot more durable and solid than fishing line, so you're less likely to have problems with it breaking or tangling.
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Re: Protein Modeling C

Postby starpug on Thu Sep 01, 2011 10:26 pm

Is suspending/building something to display the protein all that important? I mean yes it helps transport an keep the protein in a specific shape, but do you think judges view it as contributing to your model?
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Re: Protein Modeling C

Postby rfscoach on Sat Sep 03, 2011 9:07 am

starpug wrote:Is suspending/building something to display the protein all that important? I mean yes it helps transport an keep the protein in a specific shape, but do you think judges view it as contributing to your model?


It is not in the judging rubric, so, no.
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Re: Protein Modeling C

Postby butter side up on Sun Sep 04, 2011 8:46 pm

rfscoach wrote:
starpug wrote:Is suspending/building something to display the protein all that important? I mean yes it helps transport an keep the protein in a specific shape, but do you think judges view it as contributing to your model?


It is not in the judging rubric, so, no.

No- we don't have it as a contributing part of our model, just to help keep it structurally sound. When we went to impound it, we would prop it up with skewers stuck in the base (which was decorated with things having to do with the protein) and then we could do things like make final adjustments to any deformations that may have happened en route, such as bending of the structure and the amino acids being pushed towards the wrong direction. With it supported, we could be sure that everything would remain as we wanted until the judges got to inspect it.
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Re: Protein Modeling C

Postby XXGeneration on Tue Sep 06, 2011 9:07 pm

Hello all, as I am completely new to this event and everything seems so daunting, from the wiki to the test exchange to the threads, does anyone know any good websites or resources to introduce me to protein modeling?
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Re: Protein Modeling C

Postby Phenylethylamine on Wed Sep 07, 2011 2:25 pm

XXGeneration wrote:Hello all, as I am completely new to this event and everything seems so daunting, from the wiki to the test exchange to the threads, does anyone know any good websites or resources to introduce me to protein modeling?

The Center for Biomolecular Modeling at MSOE has a great site that's specific to SciO protein modeling: http://cbm.msoe.edu/stupro/so/index.html. That's a good place to start; it's got an overview of the event as well as a lot of more specific information.
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Re: Protein Modeling C

Postby XXGeneration on Wed Sep 07, 2011 8:20 pm

How would I begin to study for the written portion of the test?
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