Protein Modeling C

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Phenylethylamine
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Re: Protein Modeling C

Postby Phenylethylamine » March 21st, 2011, 2:20 pm

Also, a belated congratulations; I assume you're the former-competitor-turned-supervisor who the lady handing out medals referred to as having "won the event in the past". I didn't know this had been an event prior to last year.
I think it was the Astronomy supervisor that they were talking about.
I don't think so; this was when I went up for my medal in Protein Modeling, and she said "this event". I don't know what she was talking about, then, but her exact words were, "You know, if you're good at this stuff, you can get all sorts of jobs and do well. One of the supervisors this year won the event a few years back, and now he's at Yale studying something similar." (Maybe I shouldn't say "exact words", since I don't know that I remember it exactly, but that was the gist of it.)

kwijiborjt, will you still be the Pro Mod supervisor next year?

Also, I'm really wondering who it was that I talked to on stage. I think they were from the second place team. Any of you?
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Re: Protein Modeling C

Postby kwijiborjt » March 21st, 2011, 3:45 pm

Yeah there was a mistake. I am at Yale so it was probably about me, but I didn't win this event. I'm a senior now and this is only the second year of the event.

I'm not sure if i'm running it next year. The competition won't be at West Point next year, because they're doing renovations. I also don't know where I'll be living next year, as I'm currently looking for a job.
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Re: Protein Modeling C

Postby TheWiseGirl » March 21st, 2011, 9:57 pm

I just want to make sure I got this right; so the state tests are generally all the same, but the supervisor can edit it to their discretion, correct?
And also, is the protein modeled at state the "homeo-domain Nanog" protein? I found in on the MSOE website, but I want to make sure that's the one.

Did anyone else get the adenovirus question at regionals? Who thought that was kind of random?

On another note, I feel so out of the loop! All you peoples in New York seem to know each other. I, on the other hand, am stranded in good ol' Washington State with the Rain. :) And does NY have their state competition relatively early? Ours is in 3 weeks. I feel behind.
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Re: Protein Modeling C

Postby paradoxgirl » March 22nd, 2011, 1:04 pm

A question for kwijiborjt:
Since you picked out five of the bases that were involved with binding (i think there may have been one or two more if you look in jmol)
On the jmol for the prebuild, 10 DNA bases are shown. Are you talking about file 2wbu or 2wbs? 2wbs shows only 7 bases, and a slightly different sequence than the one in our prebuild environment. I'm trying to figure out specifically where the hydrogen bonds are, (between which side chains and bases)
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Re: Protein Modeling C

Postby Phenylethylamine » March 22nd, 2011, 3:36 pm

And also, is the protein modeled at state the "homeo-domain Nanog" protein? I found in on the MSOE website, but I want to make sure that's the one.
The Nanog on the MSOE website is the right one, yes.
Did anyone else get the adenovirus question at regionals? Who thought that was kind of random?
Adenoviruses/lentiviruses/retroviruses are relevant to the event because viral vectors are used to introduce the genes for the iPSC proteins into the host cells. You should definitely research them- there's a good chance they'll continue to show up at every level of competition.
And does NY have their state competition relatively early? Ours is in 3 weeks. I feel behind.
I think New York has the earliest States for C Division.
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Re: Protein Modeling C

Postby nanowhale » March 22nd, 2011, 10:04 pm

Illinois doesn't have State until April 16th... before reading all of this I thought I knew a lot after not so much.... guess it was a reality check. Time to brush up on my knowledge
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Re: Protein Modeling C

Postby TheWiseGirl » March 23rd, 2011, 1:30 am

And also, is the protein modeled at state the "homeo-domain Nanog" protein? I found in on the MSOE website, but I want to make sure that's the one.
The Nanog on the MSOE website is the right one, yes.
Did anyone else get the adenovirus question at regionals? Who thought that was kind of random?
Adenoviruses/lentiviruses/retroviruses are relevant to the event because viral vectors are used to introduce the genes for the iPSC proteins into the host cells. You should definitely research them- there's a good chance they'll continue to show up at every level of competition.
And does NY have their state competition relatively early? Ours is in 3 weeks. I feel behind.
I think New York has the earliest States for C Division.
Thanks! I'll be sure to brush up on my viruses. And stem cell terminology.
Hm, so I guess the better way to put it is that we're "on time" here in Washington. New York is just early. :D
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Re: Protein Modeling C

Postby kwijiborjt » March 23rd, 2011, 2:09 pm

I think the chat about the exams and specifics of the pre-builds should be kept to a minimum on this board. This is definitely my fault for talking about my scoring guidelines. Balancing transparency and fairness between states is tricky.

To find hydrogen bonding residues, I took a close look at all the bases on the DNA in the 2wbu file and looked for amino acids that were close enough to be hydrogen bonded. Then I tried to find pairs of hydrogen bond donors and acceptors that were a bond length or so away from each other and pointed at each other. I don't remember exactly how many residues i found with hydrogen bonding, but i think it was about seven or eight. If any of this doesn't make sense to you, you should research it for yourself instead of expecting other competitors to give you answers!

I will say that i was kind of displeased that pretty much nobody in New York knew how hydrogen bonding actually works. This would definitely be a good topic to study in great detail, as it's critical to understanding any protein, and will certainly come up on exams and in your pre-builds every year.
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Re: Protein Modeling C

Postby The Eviscerator » March 28th, 2011, 12:33 pm

Hey everyone
I just got added to this event if my team makes nationals (hopefully).
So can someone explain the process of the on-site build? I'm not sure how that works out.
Also, what programs do we need to know how to use. So far I only know about jmol.
All help will be greatly appreciated!

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Re: Protein Modeling C

Postby Phenylethylamine » March 28th, 2011, 12:55 pm

Hey everyone
I just got added to this event if my team makes nationals (hopefully).
So can someone explain the process of the on-site build? I'm not sure how that works out.
Also, what programs do we need to know how to use. So far I only know about jmol.
All help will be greatly appreciated!
For the on-site build, you're given a Jmol environment (which should look almost exactly like the pre-build environment on the CBM site, except it will be a different protein) with the file specified in the rules (at Nationals, it will be c-Myc, PDB ID 1NKP). The sidebar of the competition environment will specify what part of the given protein you should model, and which sidechains you should display. It will also have a section telling you what materials you should have received; the supervisor will give you an envelope containing those materials (the correct size of Mini-Toober, end caps, the appropriate sidechains, and cross-linkers). You can manipulate the Jmol image any way you want, and then use it as a "map" to bend the Mini-Toober into the correct conformation.

Jmol is the only program used for this event, although at my Regional tournament, we were also given the option of working in RasMol (which had been loaded onto all the computers used for the event) if we didn't like the online competition environment (which personally I don't). At most competitions, though, this option is unlikely to be available. RasMol is basically the same thing as Jmol, anyway, although some of the commands are a bit different.
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