Protein Modeling C

User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Location: Harvard University

Re: Protein Modeling C

Postby Phenylethylamine » September 26th, 2010, 3:21 pm

I'm just curious, but have you guys started your pre-build yet?

My team is (kinda) off to a slow start this year and I was curious what sets you guys are building with.

I am currently looking at the Amino Acid Starter Kit (My god it's expensive and shipping is pricey...) is this the set I should get to begin with? I don't want to mispurchase something like this.

Thank you for reading and helping~!
I haven't started my pre-build yet, but that's mainly because I'm submitting a paper to the Siemens-Westinghouse competition about four days from now... I'll be starting as soon as I catch up with all the work I pushed back for the sake of this project xD.

Given that it's not even October yet and the earliest competitions aren't until February or so, I don't think you need to worry about your team being off to a slow start just yet.

I wouldn't order the Amino Acid Starter Kit if I were you- it has a lot of stuff you don't need, and the Mini-Toober it comes with isn't the right length. Unfortunately, I don't know where to get the correct set; last year, they provided every team with one for free, and while I'd have to assume they won't do that this year, I'd guess there'll be a special set with the correct length of Mini-Toober available somehow. I'll try to get back to you on that one once I've figured it out myself.
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009

User avatar
Lily Essence
Member
Member
Posts: 67
Joined: March 29th, 2009, 1:36 pm
Division: C
State: TX

Re: Protein Modeling C

Postby Lily Essence » September 28th, 2010, 4:48 pm

I haven't started my pre-build yet, but that's mainly because I'm submitting a paper to the Siemens-Westinghouse competition about four days from now... I'll be starting as soon as I catch up with all the work I pushed back for the sake of this project xD.

Given that it's not even October yet and the earliest competitions aren't until February or so, I don't think you need to worry about your team being off to a slow start just yet.

I wouldn't order the Amino Acid Starter Kit if I were you- it has a lot of stuff you don't need, and the Mini-Toober it comes with isn't the right length. Unfortunately, I don't know where to get the correct set; last year, they provided every team with one for free, and while I'd have to assume they won't do that this year, I'd guess there'll be a special set with the correct length of Mini-Toober available somehow. I'll try to get back to you on that one once I've figured it out myself.
Thanks for the tip. I didn't know that teams were given a set by SO last year. We'll probably have to buy ours; I don' t think they'll give these free again. :P

On a side note, in Texas, our first invitational is November 20, so I was just getting a little antsy. XD
Silent and Listen are spelled with the same letters
Seven Lakes SLHS Science Olympiad
Retiring my competition career! Off to scold the newbies as a manager!

GCXC
Member
Member
Posts: 44
Joined: April 19th, 2010, 6:16 pm
Division: C
State: TX
Location: C-W

Re: Protein Modeling C

Postby GCXC » September 28th, 2010, 6:53 pm

yea i just cut mine from last year to the right length and i used pipecleaners/push pins to show all my significant sidechains i just need to write my description,etc on the note card otherwise im pretty much ready... i think :?
2012 State:
1st Robot Arm
2nd Protein Modeling
3rd Microbe Mission

Flavorflav
Member
Member
Posts: 1364
Joined: February 5th, 2006, 7:06 am
Division: Grad
State: NY

Re: Protein Modeling C

Postby Flavorflav » September 29th, 2010, 6:59 am

last year, they provided every team with one for free, and while I'd have to assume they won't do that this year, I'd guess there'll be a special set with the correct length of Mini-Toober available somehow. I'll try to get back to you on that one once I've figured it out myself.
Confirmed - we will not be supplied with kits this year. They are available for purchase from 3d molecular designs, but the price has not been fixed yet: http://www.3dmoleculardesigns.com/scienceolympiad.asp

gsheni
Member
Member
Posts: 23
Joined: January 28th, 2009, 4:06 pm
Division: C

Re: Protein Modeling C

Postby gsheni » October 5th, 2010, 7:44 am

Can someone tell me the residues. I have that it is chain A and it is 85 amino acids

User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Location: Harvard University

Re: Protein Modeling C

Postby Phenylethylamine » October 5th, 2010, 2:24 pm

Can someone tell me the residues. I have that it is chain A and it is 85 amino acids
The section to be built for the pre-build model is all of chain A of 2WBU.pdb. The entire chain is 85 residues in length, as you can see here.
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009

User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Location: Harvard University

Re: Protein Modeling C

Postby Phenylethylamine » October 5th, 2010, 2:56 pm

last year, they provided every team with one for free, and while I'd have to assume they won't do that this year, I'd guess there'll be a special set with the correct length of Mini-Toober available somehow. I'll try to get back to you on that one once I've figured it out myself.
Confirmed - we will not be supplied with kits this year. They are available for purchase from 3d molecular designs, but the price has not been fixed yet: http://www.3dmoleculardesigns.com/scienceolympiad.asp
Although the kits don't appear to be in the 3D Molecular Designs online catalog yet, they can be ordered by email here, product code SOPB10, for $12 each, $6 shipping for the first set and $2 for each additional one.
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009

Flavorflav
Member
Member
Posts: 1364
Joined: February 5th, 2006, 7:06 am
Division: Grad
State: NY

Re: Protein Modeling C

Postby Flavorflav » October 6th, 2010, 7:15 am

Can someone tell me the residues. I have that it is chain A and it is 85 amino acids
The section to be built for the pre-build model is all of chain A of 2WBU.pdb. The entire chain is 85 residues in length, as you can see here.
Following your link, I see the length stated as 90 residues. Am I missing something? I also see that the first five (GSRTA) are not underlined. Are those the five to be left out?

User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Location: Harvard University

Re: Protein Modeling C

Postby Phenylethylamine » October 6th, 2010, 5:09 pm

Can someone tell me the residues. I have that it is chain A and it is 85 amino acids
The section to be built for the pre-build model is all of chain A of 2WBU.pdb. The entire chain is 85 residues in length, as you can see here.
Following your link, I see the length stated as 90 residues. Am I missing something? I also see that the first five (GSRTA) are not underlined. Are those the five to be left out?
Sorry if that was confusing- only residues that they have structural data for can be modeled, so only residues 399-483 are to be included. The stated length is 90 residues, but like you said, the first five aren't underlined- that is, they're not actually visible in the PDB file. This means we know what those residues are, but not where they are, so we can't show them in a model. Therefore, chain A of 2WBU.pdb is effectively 85 residues in length.
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009

User avatar
JustDroobles
Member
Member
Posts: 162
Joined: February 9th, 2009, 3:28 pm
Division: Grad
State: MI
Location: WI

Re: Protein Modeling C

Postby JustDroobles » October 23rd, 2010, 11:31 am

After reading the rules I don't understand why a team of three is required to do this event... Although I have never competed in Protein Modeling so maybe there is more work than I thought. Do you have the whole testing time to work on the written test and the model, or are these sections split up and timed? Or would there generally be one person working on the model and one person working on the test, and one person helping the others?


Return to “2011 Lab Events”

Who is online

Users browsing this forum: No registered users and 1 guest