Protein Modeling C [NY Trial]

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Protein Modeling C [NY Trial]

Postby Jim_R » Mon Aug 17, 2009 8:56 pm

Discussion for Protein Modeling C, a trial event in New York.

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Re: Protein Modeling C [NY Trial]

Postby Flavorflav » Sun Sep 13, 2009 1:33 pm

The rules linked to above are notthe correct rules for this event. Those are the draft rules from June. The final rules are here. The biggest difference are that the molecules have changed and only two students may compete.

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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » Sun Oct 04, 2009 3:32 pm

Is this being run at any Regional competitions, or just at States? Because I'm pretty sure my region isn't running it- not really surprising, since it's pretty heavy on the setup.
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Re: Protein Modeling C [NY Trial]

Postby Flavorflav » Tue Oct 06, 2009 2:06 am

Phenylethylamine wrote:Is this being run at any Regional competitions, or just at States? Because I'm pretty sure my region isn't running it- not really surprising, since it's pretty heavy on the setup.

All regions are supposed to run the trial events. If they don't, they get fewer medals from the State. I am quite sure that E.L.I. will run it.

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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » Tue Oct 06, 2009 9:39 pm

Flavorflav wrote:
Phenylethylamine wrote:Is this being run at any Regional competitions, or just at States? Because I'm pretty sure my region isn't running it- not really surprising, since it's pretty heavy on the setup.

All regions are supposed to run the trial events. If they don't, they get fewer medals from the State. I am quite sure that E.L.I. will run it.

Yeah, I was told that the region always runs the trials, although nobody was sure why. That's good to know.
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Re: Protein Modeling C [NY Trial]

Postby AlchemyRocks » Mon Oct 19, 2009 9:20 pm

I believe the rules for the New York Protein Modeling and Wisconsin Protein modeling are the same. Can someone confirm this for me?
Unfortunately, I am working from a school computer at the moment, and any time I click on a .pdf file, the browser quits out. No clue why this is...but I've come to except it with school computers.

If this is confirmed, I would like to know the way to obtain the Mini-Toobers materials for the building. Do we order them off the site?
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Re: Protein Modeling C [NY Trial]

Postby Flavorflav » Tue Oct 20, 2009 4:40 pm

AlchemyRocks wrote:I believe the rules for the New York Protein Modeling and Wisconsin Protein modeling are the same. Can someone confirm this for me?
Unfortunately, I am working from a school computer at the moment, and any time I click on a .pdf file, the browser quits out. No clue why this is...but I've come to except it with school computers.

If this is confirmed, I would like to know the way to obtain the Mini-Toobers materials for the building. Do we order them off the site?

I would be very surprised if they were different, because I believe trial event rules are supposed to be the same throughout the country. Clarifications made at the State level would only apply to that State, though.

You can get miniToobers at the bottom of this page: http://www.3dmoleculardesigns.com/news2.php#betafolding

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Re: Protein Modeling C [NY Trial]

Postby AlchemyRocks » Wed Nov 11, 2009 2:35 am

Thank you. : )
I got my MiniToober stuff sent to me.
Now...I'm trying to figure out how to use Jmol. : D
I love messing with new programs!
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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » Wed Nov 11, 2009 7:11 pm

AlchemyRocks wrote:Thank you. : )
I got my MiniToober stuff sent to me.
Now...I'm trying to figure out how to use Jmol. : D
I love messing with new programs!

If you're having any trouble with Jmol, there is a whole wiki on it (http://wiki.jmol.com). It's sometimes unclear, and not really designed for beginners, unfortunately, but there is a page of tutorials (http://wiki.jmol.org/index.php?title=Jmol_Tutorials) which may or may not be helpful.
I don't know if you're more comfortable with a command line setup or with using the menus, but personally I prefer the command line (although I believe full functionality is available without touching the command line). If you're looking for it, the command line can be accessed by going to File -> Output Console (it took me a while to figure out that 'Output Console' was the command line :? ). I don't know much about using the menus (because I almost never do- except to open files, since that doesn't seem to work very well in the command line for some reason), but I'm pretty familiar with the commands if you have any questions.
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Re: Protein Modeling C [NY Trial]

Postby AlchemyRocks » Thu Nov 12, 2009 11:26 pm

I'll see which works better for me. To be honest, I have nearly no background in command prompt or whatever it is.
But it can't hurt to learn new trick. Thanks for the site. I'll definately check it out!
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Re: Protein Modeling C [NY Trial]

Postby skiblack331 » Sun Jan 03, 2010 6:28 pm

I'm a little bit confused with this event. It says that we're supposed to add the side chains that are important to the protein's shape. How are we supposed to figure out which side chains are important?
I wasn't sure which ones are important, so while I was going through the steps, I went to one of the websites listed (http://www.callutheran.edu/BioDev/omm/jmol/ha/ha.html). Though it doesn't outright state the important side chains, the website gives the number of a few of the amino acids. I figured that these must be the important ones, so when I used Jmol, I input the specific protein numbers to view the specific amino acids. I found, however that according to the website above, amino acid #106 is histidine, but according to the protein database website, that amino acid is argine. Which website is right?
Also, the rules state we should build a model of Chain B, but there is not a chain listed as "B", but instead the letters "H" through "M". I used Chain M, is that the correct one to use?
I appreciate any insights anyone might have. Thanks.
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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » Wed Jan 06, 2010 7:18 pm

skiblack331 wrote:I'm a little bit confused with this event. It says that we're supposed to add the side chains that are important to the protein's shape. How are we supposed to figure out which side chains are important?
I wasn't sure which ones are important, so while I was going through the steps, I went to one of the websites listed (http://www.callutheran.edu/BioDev/omm/jmol/ha/ha.html). Though it doesn't outright state the important side chains, the website gives the number of a few of the amino acids. I figured that these must be the important ones, so when I used Jmol, I input the specific protein numbers to view the specific amino acids. I found, however that according to the website above, amino acid #106 is histidine, but according to the protein database website, that amino acid is argine. Which website is right?
Also, the rules state we should build a model of Chain B, but there is not a chain listed as "B", but instead the letters "H" through "M". I used Chain M, is that the correct one to use?
I appreciate any insights anyone might have. Thanks.

It actually says the side chains that are important to the protein's function. If you research the function of the protein, you'll probably find information about certain side chains that are specifically involved (I haven't done this research yet, but I did a similar project with a different protein, and a very little research quickly revealed which side chains were important. I'm talking Wikipedia research, and clicking a few of the links at the bottom of the page. Not too in-depth).

To find out what residue 106 actually is, select it in Jmol and look at its three-letter amino acid code. However, I'm thinking that since you're seeing a contradiction, it's possible that you've downloaded a different file than you intended?

When I downloaded the PDB file, there was definitely a Chain B. Do you have the exact link of what you downloaded?
If you haven't already, try using the commands "select*b" or "restrict*b". If you were using another command, you may have been selecting something else; those commands will definitely work in the case that there is a B chain. Jmol can be screwy sometimes, though, so you can always try closing the file and reopening it, or redownloading it.
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Re: Protein Modeling C [NY Trial]

Postby skiblack331 » Sat Jan 09, 2010 3:27 am

Thanks for the help. I realized that none of the chains in Jmol were actually chain B, but were labeled with different letters. I'm not sure what the problem is with the contradiction, but I don't think it matters because I don't think it's that important. I read the websites we were given, but I didn't see anything about important amino acids. We were given three crosslinks with the kit, so they must have a significance, so I'll check there first.
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Re: Protein Modeling C [NY Trial]

Postby batmankiller » Wed Jan 20, 2010 4:33 am

I too, am having troubles findign the important side chains, the helices and all that were easy by the important side chains is annoying to find.. lemme know if you guys find sites for the research because I've been looking and not having any luck (don't have to give me the exact amino acid #.. unless you don't mind =D.. just give me a place to look >.>)
Last edited by batmankiller on Tue Feb 02, 2010 4:53 am, edited 1 time in total.

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Re: Protein Modeling C [NY Trial]

Postby Flavorflav » Mon Feb 01, 2010 2:06 pm

batmankiller wrote:I too, am having troubles findign the important side chains, the helices and all that were easy by the important side chains is annoying to find.. lemme know if you guys find sites for the research because I've been looking and not having any luck (don't have to give me the exact amino acid #.. unless you don't mind =D.. just give me a place to look >.>)

and do we have to know about dark energy/dark matter?

For protein modeling? I wouldn't think so.


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