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Re: Protein Modeling C

Posted: October 23rd, 2010, 7:00 pm
by nanowhale
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?
You are absolutely correct about the need for 3 members because you really don't, two is actually enough, when it was a trial event last year I did it with only one other person and we did perfectly fine. Also, you only have the 50 min i believe to do both the test and model. It really is up to your coach on how many people are doing the event.

Re: Protein Modeling C

Posted: October 26th, 2010, 8:43 am
by Phenylethylamine
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?
You are absolutely correct about the need for 3 members because you really don't, two is actually enough, when it was a trial event last year I did it with only one other person and we did perfectly fine. Also, you only have the 50 min i believe to do both the test and model. It really is up to your coach on how many people are doing the event.
Although the event could certainly be done with only two people (I also competed in it as a trial last year, with just one other person, and we had plenty of time), because three-person teams are allowed this year, you would probably put yourself at a disadvantage by only bringing two people to competition.

Re: Protein Modeling C

Posted: November 11th, 2010, 10:43 am
by mathemaniac
Anyone wanna help out a SciOly newcomer with protein modeling? This is the first year our school has a strong program, and we have a lot of oppurtunity, so I really want to know how to do well.
What is the focus area for the written portion of this competition? And how can my team make our models a lot better than just the generic model with no add-ons?

Re: Protein Modeling C

Posted: November 11th, 2010, 8:26 pm
by Phenylethylamine
Anyone wanna help out a SciOly newcomer with protein modeling? This is the first year our school has a strong program, and we have a lot of oppurtunity, so I really want to know how to do well.
What is the focus area for the written portion of this competition? And how can my team make our models a lot better than just the generic model with no add-ons?
First, I recommend that you read the Protein Modeling Wiki. It's incomplete, but it will be continually updated with more information.

Second, the written portion of the competition will involve general protein structure, composition, and function questions, and specifically for this year it will also focus on induced pluripotent stem cells. (There's not very much about those on the wiki yet, but Wikipedia has some information.)

Third, for good add-ons, you should do some research on the protein you're modeling (Klf4) and figure out what its function is– and what parts of it are specifically involved in that function. You should highlight those parts, particularly any specific sidechains that interact with whatever it acts upon.

If you have any more specific questions, we would be happy to answer in greater detail.

Re: Protein Modeling C

Posted: November 23rd, 2010, 4:29 pm
by GCXC
i know this is a bit late to ask but did anyone go to any of the S.O training clinics and might have done anything on protein modeling?

Re: Protein Modeling C

Posted: December 8th, 2010, 7:18 am
by Starapollo1
Okay I don't know if anyone else has been to a competition yet but when we went we never got a score for our prebuild or on site. They were graded and were counted towards our scores but the judge/proctor never gave us the results for anything except the onsite exam... has this happened to anyone else? Is this the norm? I was just bummed cause I worked really hard on the prebuild and I wanted to see how it did... Overall though I felt the competition was a really good one, the test was espicially awesome!

Re: Protein Modeling C

Posted: December 8th, 2010, 1:46 pm
by ajwilliams2011
Hi, I am a four year Sci O member and I have had success all four years but this year I have been thrown for a loop...

Protein Modeling is driving my team and I crazy. We have read and read and read but we are clueless as to how to make the computer model into a 3-D, physical model. Maybe it's really simply and we are just missing something small...but we really need some guidance!!

Anyone who can help, please send me a message on here! =]

Thanks!

Re: Protein Modeling C

Posted: December 8th, 2010, 2:33 pm
by EastStroudsburg13
I've never done this before, but the way I'm approaching it is to figure out the components of the chain first, and then work on creating its shape. The Jmol takes a little getting used to if you haven't used something like it before but you'll get the hang of it. You can use the link to the reference sheet at the top of the Jmol window for help.

I just need one clarification. The DNA present in the computer model: that counts as a extra thing for the model, right? And would we have it separate from the protein or intertwine it in some way?

Re: Protein Modeling C

Posted: December 8th, 2010, 6:03 pm
by Starapollo1
I've never done this before, but the way I'm approaching it is to figure out the components of the chain first, and then work on creating its shape. The Jmol takes a little getting used to if you haven't used something like it before but you'll get the hang of it. You can use the link to the reference sheet at the top of the Jmol window for help.

I just need one clarification. The DNA present in the computer model: that counts as a extra thing for the model, right? And would we have it separate from the protein or intertwine it in some way?
Alrigt, so I say YES the DNA is an addition, and my coach agrees one hundred percent, BUT i can't know for sure cause none of my proctors have given us a score sheet back for the pre build. If you want anymore specifics just message me, even though none of my proctors haven't given me score sheets i've placed every time in the top 5 so I'm assuming I'm doing something right...

Re: Protein Modeling C

Posted: December 10th, 2010, 9:02 am
by EastStroudsburg13
Okay so I'll focus on the protein for now. Thanks. :)