Protein Modeling C

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Re: Protein Modeling C

Post by EastStroudsburg13 » November 11th, 2011, 8:32 am

Well, this is one reason the on-site build is only 30% of the event.

At regionals, they will almost certainly have actual Toobers for modeling. If they don't, well, then there's something wrong, since it's not like an invite, which is just practice. The major invites like Solon and Mentor will also probably have Toobers, but some of the less commonly-attended ones might not, and you'll have to deal with that. It actually might be good practice to have to deal with something that doesn't hold its shape as well.

I think it is necessary to have 3. You have to deal with both the test and the model at the same time, and in order to model the protein quickly, sometimes you have to have 2 people working together. Then, the third person can work on the test, and if there's time, the you can go over the test together and tweak your model. I think, with only 2 people, they would both have to be very strong (and be able to work independently) in the event, otherwise you may run out of time trying to focus on one part and not the other.

I don't know about textbooks personally. Phenyl might have suggestions, but I'd just say that an AP Bio book might be helpful with regards to general protein information. Other than that, the Internet is your friend. :)
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Re: Protein Modeling C

Post by Phenylethylamine » November 11th, 2011, 3:21 pm

EASTstroudsburg13 wrote:I think it is necessary to have 3. You have to deal with both the test and the model at the same time, and in order to model the protein quickly, sometimes you have to have 2 people working together. Then, the third person can work on the test, and if there's time, the you can go over the test together and tweak your model. I think, with only 2 people, they would both have to be very strong (and be able to work independently) in the event, otherwise you may run out of time trying to focus on one part and not the other.
The NY State people have already stated that teams will only get two students on the event at States. Personally, I think that should be fine – I did the event as a trial two years ago, when it was only two people, anyway. Have one person put together the onsite, the other work on the test, and then when the onsite is finished, switch – the other person can check over the onsite, and the one who did the onsite can fill in anything on the test that the first person didn't get.
EASTstroudsburg13 wrote:I don't know about textbooks personally. Phenyl might have suggestions, but I'd just say that an AP Bio book might be helpful with regards to general protein information. Other than that, the Internet is your friend. :)
For the specifics of the prebuild and onsite, I'd recommend reading the PDB primary citation, as well as searching the PDB ID on Google Scholar to find other papers about the protein. They can be a little dense, but that's the best way to find out what residues are important to the protein's function, and in what way. Also, get familiar with Jmol, and use it to look at the protein until you know the structure backwards and forwards (if you download standalone Jmol, you can look at the onsite in advance, too).

Sorry, I can't recommend any textbooks; I don't use them, myself. The Internet, as EASTstroudsburg said, is your friend.
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Re: Protein Modeling C

Post by XXGeneration » November 13th, 2011, 3:01 pm

Does anyone have any ideas for creative additions this year? All that I can really think of are marking the active sites and the secondary structures.. would putting in the hydrogen bonds be of any help? Or of the proteins that the caspase works with?

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Re: Protein Modeling C

Post by Phenylethylamine » November 13th, 2011, 5:29 pm

XXGeneration wrote:Does anyone have any ideas for creative additions this year? All that I can really think of are marking the active sites and the secondary structures.. would putting in the hydrogen bonds be of any help? Or of the proteins that the caspase works with?
Sadly, I haven't gotten that far yet. Get back to me in about a month, when Intel submission has passed and I'm between waves of college apps >.<
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Re: Protein Modeling C

Post by XXGeneration » November 13th, 2011, 5:36 pm

Phenylethylamine wrote:
XXGeneration wrote:Does anyone have any ideas for creative additions this year? All that I can really think of are marking the active sites and the secondary structures.. would putting in the hydrogen bonds be of any help? Or of the proteins that the caspase works with?
Sadly, I haven't gotten that far yet. Get back to me in about a month, when Intel submission has passed and I'm between waves of college apps >.<
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Is there any good number for creative additions?

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Re: Protein Modeling C

Post by Phenylethylamine » November 14th, 2011, 4:37 pm

XXGeneration wrote:
Phenylethylamine wrote:
XXGeneration wrote:Does anyone have any ideas for creative additions this year? All that I can really think of are marking the active sites and the secondary structures.. would putting in the hydrogen bonds be of any help? Or of the proteins that the caspase works with?
Sadly, I haven't gotten that far yet. Get back to me in about a month, when Intel submission has passed and I'm between waves of college apps >.<
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Is there any good number for creative additions?
There's a limit to the total number of points judges can give for creative additions, and there's a limit to how many points they can give for any particular addition (I'm not sure if this is official, but in practice I think it's true either way); if I recall correctly, it works out to 6-8 creative additions, tops. Some judges will only give credit for up to four. It's not that you'll be penalized for having more than that; it's just unlikely to help you. I'll try to have four or five good ones for Regionals, and add from there.

Number of additions probably isn't the most important factor. Sure, you don't want to have too few, and you don't want to have anything on there that doesn't contribute to the "molecular story", but how you execute your additions is important as well. For example, last year, nearly everyone showed the DNA bound to Klf4. The trick was to display it in a way that was clear, accurate (e.g., to scale), useful in specific understanding of how it was bound (e.g., hydrogen bond contacts between residues and nucleotides correctly placed), and as icing on the cake, aesthetically pleasing. [I keep meaning to take and post photos of my model from last year on the Image Gallery, but haven't gotten around to it. Note to self: do that. I think some other people have posted prebuild photos from last year, though.]
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Re: Protein Modeling C

Post by akatsuki9 » November 14th, 2011, 5:37 pm

Do the judges give you feedback on your pre-build model?
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Re: Protein Modeling C

Post by Phenylethylamine » November 14th, 2011, 6:08 pm

akatsuki9 wrote:Do the judges give you feedback on your pre-build model?
Not typically. If it's Regionals, you might be able to ask them nicely about it if you have time after the competition. Otherwise, you'll probably only get feedback if you know a judge from something outside the competition.
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Re: Protein Modeling C

Post by EastStroudsburg13 » November 15th, 2011, 8:40 am

Phenylethylamine wrote:
akatsuki9 wrote:Do the judges give you feedback on your pre-build model?
Not typically. If it's Regionals, you might be able to ask them nicely about it if you have time after the competition. Otherwise, you'll probably only get feedback if you know a judge from something outside the competition.
Sometimes you'll get notes from an invitational tournament. I think we got some from Athens last year, although I'm not too confident. Usually you'll just get the rubric or not even that, though, and that's only for invites. So other than that, unless you contact your supervisor afterwards, you probably won't get feedback.
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Re: Protein Modeling C

Post by Starapollo1 » November 21st, 2011, 9:43 am

I'm having incredible difficulties isolating the two polypeptides we are supposed to model... Upon going to the the prebuild page: [urlhttp://cbm.msoe.edu/includes/jmol/SOJmols/2012PreBuild.html[/url], I tried "restrict chain A" and "restrict chain B" along with multiple variations of the command... and I can't seem to get it to work... the answer is probably really simple but I just can't seem to figure it out.
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