Protein Modeling C

Re: Protein Modeling C

Postby Phenylethylamine on Tue Oct 25, 2011 7:12 pm

bocahighscienceolypm wrote:
They have a link to a PDF that shows how the numbering actually goes (this information should also be on the PDB structure summary page, but I'm currently getting an error when I try to look at this or any other structure summary in the PDB). If you're trying to number your Toober from 148 straight through to 296, you'll run out of Toober; make sure you follow the actual numbering of the file.


Amino acids (for chain B) 310-401 do not exist in the pdb file. Can anyone help?
How are you finding that they "do not exist"? When I look at the pdb file, they are there.

Try opening the PDB in Jmol (or going to the online prebuild environment, I don't know what you prefer to use) and, before typing anything else, type "restrict *b and 310-401". Chain B – amino acids 310 through 401 – should appear.

If this doesn't work, there are a couple possibilities I've thought of: if you're using standalone Jmol on your computer and have downloaded the PDB file, I suppose it is possible that your download was cut short and you're missing part of the file... in which case you could try re-downloading the file. If you're using the online environment or are using standalone Jmol but are certain that all your downloads were complete, my best guess is that you used a command that caused chain B to be excluded (e.g., "restrict *a") and then afterwards tried to look at chain B. Try "select all", then "backbone" (or any other viewing command, just to get everything visible again), and then "restrict *b and 310-401".
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Re: Protein Modeling C

Postby bocahighscienceolypm on Thu Oct 27, 2011 3:44 pm

Phenylethylamine wrote:
bocahighscienceolypm wrote:
They have a link to a PDF that shows how the numbering actually goes (this information should also be on the PDB structure summary page, but I'm currently getting an error when I try to look at this or any other structure summary in the PDB). If you're trying to number your Toober from 148 straight through to 296, you'll run out of Toober; make sure you follow the actual numbering of the file.


Amino acids (for chain B) 310-401 do not exist in the pdb file. Can anyone help?
How are you finding that they "do not exist"? When I look at the pdb file, they are there.

Try opening the PDB in Jmol (or going to the online prebuild environment, I don't know what you prefer to use) and, before typing anything else, type "restrict *b and 310-401". Chain B – amino acids 310 through 401 – should appear.

If this doesn't work, there are a couple possibilities I've thought of: if you're using standalone Jmol on your computer and have downloaded the PDB file, I suppose it is possible that your download was cut short and you're missing part of the file... in which case you could try re-downloading the file. If you're using the online environment or are using standalone Jmol but are certain that all your downloads were complete, my best guess is that you used a command that caused chain B to be excluded (e.g., "restrict *a") and then afterwards tried to look at chain B. Try "select all", then "backbone" (or any other viewing command, just to get everything visible again), and then "restrict *b and 310-401".


It was something odd with the commands we were using, thanks for the advice.
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Re: Protein Modeling C

Postby akatsuki9 on Thu Nov 10, 2011 4:46 pm

Hey,

At my first invitational, they gave us pipe cleaners for the on-site model. Will they give us a minitoober(s) for district? The pipe cleaners aren't that great for a protein model because they don't keep their shape as well.
Also, are there any good textbooks out there to study from for this event?
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Re: Protein Modeling C

Postby Lily Essence on Fri Nov 11, 2011 12:23 am

I know this thread is not the place to complain about an event, but I am deeply disappointed in the amount of on-site builds this year (yet again).

Last year, as the first year this event came out, the only times I ever got to model were for state (nervous as heck since it was my first onsite build... AT STATE), and nationals, despite also going to regionals and two invitationals. The kits for the onsite builds were purchasable from the website. I passed this off as an unforeseen complication since the event was new, and asked the proctors at nationals about it. On the sheet asking about my experience, I commented on how there just wasn't enough onsite building experience available, whether the problem be price or something else.

This year, the kits are being sold at cost, and sadly both of the invitationals that my team is going to isn't offering a true "on-site build". One offered pipecleaners and an extremely simple protien, the other is telling competitors that there will be no onsite build a head of time. Hopefully, my regionals will offer a proper onsite build, but honestly, this isn't the way to run such a planned event.

What are you guys' experience with the whole on-site build portion of the exam? Is it really necessary to have 3 people for just a onsite test?
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Re: Protein Modeling C

Postby akatsuki9 on Fri Nov 11, 2011 11:10 am

Lily Essence wrote:I know this thread is not the place to complain about an event, but I am deeply disappointed in the amount of on-site builds this year (yet again).

Last year, as the first year this event came out, the only times I ever got to model were for state (nervous as heck since it was my first onsite build... AT STATE), and nationals, despite also going to regionals and two invitationals. The kits for the onsite builds were purchasable from the website. I passed this off as an unforeseen complication since the event was new, and asked the proctors at nationals about it. On the sheet asking about my experience, I commented on how there just wasn't enough onsite building experience available, whether the problem be price or something else.

This year, the kits are being sold at cost, and sadly both of the invitationals that my team is going to isn't offering a true "on-site build". One offered pipecleaners and an extremely simple protien, the other is telling competitors that there will be no onsite build a head of time. Hopefully, my regionals will offer a proper onsite build, but honestly, this isn't the way to run such a planned event.

What are you guys' experience with the whole on-site build portion of the exam? Is it really necessary to have 3 people for just a onsite test?

See my above post.
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Re: Protein Modeling C

Postby EastStroudsburg13 on Fri Nov 11, 2011 12:32 pm

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

Postby Phenylethylamine on Fri Nov 11, 2011 7:21 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

Postby XXGeneration on Sun Nov 13, 2011 7:01 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

Postby Phenylethylamine on Sun Nov 13, 2011 9:29 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

Postby XXGeneration on Sun Nov 13, 2011 9:36 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 >.<


T-T

Is there any good number for creative additions?
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Re: Protein Modeling C

Postby Phenylethylamine on Mon Nov 14, 2011 8:37 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 >.<


T-T

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

Postby akatsuki9 on Mon Nov 14, 2011 9:37 pm

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

Postby Phenylethylamine on Mon Nov 14, 2011 10:08 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

Postby EastStroudsburg13 on Tue Nov 15, 2011 12:40 pm

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

Postby Starapollo1 on Mon Nov 21, 2011 1:43 pm

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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