Protein Modeling C

[FullMetalMaple]

Based on the thread suggestions, I modeled Chain C,D. Now I want to show these as creative additions.
How would I show that?
I can show Chain E inhibiting Chain A,B. But what about Chain C,D?
Or
Should I leave out the chain C,D?

What you want to do is really up to you - they're creative additions for a reason. Looking at the national rubric from 2010 should help you because that year, another part of the Jmol file could be modeled as a creative addition.

Also, there's a chain of XIAP for each unit of caspase-3.

Sorry if I don't seem too helpful: I don't want to give away everything to others because your model is your own. It's not mine. (Also, I seem to mess up a lot with the advice I give people here. XD)

EDIT: Also, for those who wanted to read this article on PARP, it's now viewable.

[Phenylethylamine]

Based on the thread suggestions, I modeled Chain C,D. Now I want to show these as creative additions.
How would I show that?
I can show Chain E inhibiting Chain A,B. But what about Chain C,D?
Or
Should I leave out the chain C,D?

What you want to do is really up to you - they're creative additions for a reason. Looking at the national rubric from 2010 should help you because that year, another part of the Jmol file could be modeled as a creative addition.

As a general rule, anything else in the Jmol file is a good place to start looking for potential creative additions. As for how to show chains C and D, the best place to start would be by simply placing them correctly relative to your model of chains A and B. Remember, chains C and D are identical to chains A and B – all their interactions (with each other, and with things around them) are the same, too. I don't recommend showing the exact same things on both copies, though, as that's pretty much redundant and doesn't add anything new to your model. You could just let your chains C and D be a creative addition on their own without any additional adornment.

Also, there's a chain of XIAP for each unit of caspase-3.

Yes, as I think was mentioned earlier in this thread, chain E is the XIAP molecule inhibiting the caspase-3 unit made up by chains A and B; chain F is the XIAP molecule inhibiting the caspase-3 unit made up by chains C and D. Although note that this doesn't mean you have to show both, even if you are showing both units of caspase-3.

Sorry if I don't seem too helpful: I don't want to give away everything to others because your model is your own. It's not mine. (Also, I seem to mess up a lot with the advice I give people here. XD)

Hey, I don't want to give you the impression that the advice you're giving is wrong – it's usually right! But sometimes I think of something related that you just didn't mention, and I feel like I can add to your answer. Doesn't mean what you said was wrong

[FullMetalMaple]

Sorry if I don't seem too helpful: I don't want to give away everything to others because your model is your own. It's not mine. (Also, I seem to mess up a lot with the advice I give people here. XD)

Hey, I don't want to give you the impression that the advice you're giving is wrong – it's usually right! But sometimes I think of something related that you just didn't mention, and I feel like I can add to your answer. Doesn't mean what you said was wrong

No problem! I wasn't getting that impression - I appreciate that you add to what I say. It's helpful for everyone.

[Dragonshark]

We got second in this event at States, only losing by three-fourths of a point...

[Phenylethylamine]

I spent between twenty and forty hours on my prebuild between Regionals and States, adding multiple creative additions and a huge amount of detail; I read all about PARP, and we came out of the test/onsite feeling that we completely nailed both. We were certain we'd medaled, and thought we had a significant chance of the elusive first place.

So we were rather surprised when we didn't medal, and turned out to have gotten ninth.

In retrospect, I'm guessing this was my fatal mistake: I didn't realize that it wasn't going to be the same event supervisor as last year. Last year's supervisor (who some of you may remember as kwijiborjt) wanted detail, detail, detail – chemically accurate, high-level creative additions. So that's how I built my model, with heteroatoms of relevant residues shown in CPK colors, and different colored thread corresponding to different types of bonds between residues, and so on. I tried to make my creative additions creative, with some more complex stuff in addition to the obvious additions, trying to show a deeper understanding of the protein's function. And I think some of it may have gone over the heads of the judges, who were probably judging the event for the first time and adhering exactly to the grading guidelines issued by MSOE. My more advanced creative additions wouldn't have been on the list of likely/suggested creative additions (which event supervisors are encouraged to look beyond at their own discretion), and may not have received any points. Similarly, my explanations for why the highlighted residues in the onsite were important (which came straight from the primary citation for 3OD8.pdb) may have been too technical and might not have gotten as many points as a more general explanation.

It's a shame – I think this is a better event when there's room to push your understanding farther – but at the same time, it's a good reminder that you should never rely too heavily on a particular supervisor's grading/writing style for your strategy in any event.

[FullMetalMaple]

Yikes. Sorry it didn't go as well as you'd hoped, both of you.

It's a shame – I think this is a better event when there's room to push your understanding farther – but at the same time, it's a good reminder that you should never rely too heavily on a particular supervisor's grading/writing style for your strategy in any event.

I agree. When I competed in my school's invitational this year, the supervisor (my coach for this event) only graded pre-builds on the sequence of secondary structures she got off the PDB. It bothered me, because as you said, you should push your understanding further, much further than just if you can fold things in the correct order. I mean, sure, that's part of it. But I think creative additions are the heart of the pre-build.

[Dragonshark]

I spent between twenty and forty hours on my prebuild between Regionals and States, adding multiple creative additions and a huge amount of detail; I read all about PARP, and we came out of the test/onsite feeling that we completely nailed both. We were certain we'd medaled, and thought we had a significant chance of the elusive first place.

So we were rather surprised when we didn't medal, and turned out to have gotten ninth.

Sorry that it didn't go as well for you this year as it did the previous one. Despite the exam and models ostensibly being "centralized" by MSOE, each event supervisor nevertheless has their own interpretation of which things are more important than others. Even if two prebuilds are equal in terms of creative additions, the judges may choose one over the other just because they like how that one is colored more. This is just an assumption, but some supervisors probably don't even count additions made of Toober and CBM magnet sidechains only because they're the "default" materials, even if they represent perfectly valid things.

Anyways, for me, the competition was extremely close. The difference between the sixth and first place teams was only 3.5 points!

[Phenylethylamine]

I spent between twenty and forty hours on my prebuild between Regionals and States, adding multiple creative additions and a huge amount of detail; I read all about PARP, and we came out of the test/onsite feeling that we completely nailed both. We were certain we'd medaled, and thought we had a significant chance of the elusive first place.

So we were rather surprised when we didn't medal, and turned out to have gotten ninth.

Sorry that it didn't go as well for you this year as it did the previous one. Despite the exam and models ostensibly being "centralized" by MSOE, each event supervisor nevertheless has their own interpretation of which things are more important than others. Even if two prebuilds are equal in terms of creative additions, the judges may choose one over the other just because they like how that one is colored more. This is just an assumption, but some supervisors probably don't even count additions made of Toober and CBM magnet sidechains only because they're the "default" materials, even if they represent perfectly valid things.

Anyways, for me, the competition was extremely close. The difference between the sixth and first place teams was only 3.5 points!

We don't get our scores back (just our places), although I'm thinking of emailing the supervisors to ask for recommendations for Nationals, so it's conceivable that I could find out my score that way.

[Flavorflav]

In retrospect, I'm guessing this was my fatal mistake: I didn't realize that it wasn't going to be the same event supervisor as last year.

We did that with Technical - we were really well prepared for the way it has been done for the last decade, but this year's was totally different. Not in a good way, either. Score depends only on proximity to final answer, and there are only three problems? What kind of scoring system is that?

[Phenylethylamine]

In retrospect, I'm guessing this was my fatal mistake: I didn't realize that it wasn't going to be the same event supervisor as last year.

We did that with Technical - we were really well prepared for the way it has been done for the last decade, but this year's was totally different. Not in a good way, either. Score depends only on proximity to final answer, and there are only three problems? What kind of scoring system is that?

Yeah, that was our problem with Technical, too. The questions were much more interesting than Harold Miller's, though... I have kind of mixed feelings about the Technical event.

It's just weird to me that who the event supervisor was could make such a difference in Protein, though – I tend to think of it as being a very consistent event, because all the tests and rubrics and everything come straight from MSOE. Of course, rubrics are highly subject to interpretation, so...

[Dragonshark]

We don't get our scores back (just our places), although I'm thinking of emailing the supervisors to ask for recommendations for Nationals, so it's conceivable that I could find out my score that way.

Our state uses the Avogadro scoring system, meaning that the places and raw scores for everything are online within hours of the competition.

[Phenylethylamine]

We don't get our scores back (just our places), although I'm thinking of emailing the supervisors to ask for recommendations for Nationals, so it's conceivable that I could find out my score that way.

Our state uses the Avogadro scoring system, meaning that the places and raw scores for everything are online within hours of the competition.

What is the Avogadro scoring system?

In New York, places are online usually the day after competition, and we get score sheets with all the places at the end of the award ceremony, but raw scores are never released (unless you know the supervisor, or occasionally some tech supervisors will post the scores for the top few devices on the boards).

[Dragonshark]

We don't get our scores back (just our places), although I'm thinking of emailing the supervisors to ask for recommendations for Nationals, so it's conceivable that I could find out my score that way.

Our state uses the Avogadro scoring system, meaning that the places and raw scores for everything are online within hours of the competition.

What is the Avogadro scoring system?

In New York, places are online usually the day after competition, and we get score sheets with all the places at the end of the award ceremony, but raw scores are never released (unless you know the supervisor, or occasionally some tech supervisors will post the scores for the top few devices on the boards).

It's a quick and easy way to keep track of SO scores. It was developed in my state (Wisconsin) and is now used in a few others. Here's the results from my States competition, for example.

[quizbowl]

We don't get our scores back (just our places), although I'm thinking of emailing the supervisors to ask for recommendations for Nationals, so it's conceivable that I could find out my score that way.

Our state uses the Avogadro scoring system, meaning that the places and raw scores for everything are online within hours of the competition.

What is the Avogadro scoring system?

In New York, places are online usually the day after competition, and we get score sheets with all the places at the end of the award ceremony, but raw scores are never released (unless you know the supervisor, or occasionally some tech supervisors will post the scores for the top few devices on the boards).

If you were wondering, Phenylethylamine, WLI C used Avogadro scoring this year - it was really efficient and awesome!

[starpug]

I spent between twenty and forty hours on my prebuild between Regionals and States, adding multiple creative additions and a huge amount of detail; I read all about PARP, and we came out of the test/onsite feeling that we completely nailed both. We were certain we'd medaled, and thought we had a significant chance of the elusive first place.

So we were rather surprised when we didn't medal, and turned out to have gotten ninth.

In retrospect, I'm guessing this was my fatal mistake: I didn't realize that it wasn't going to be the same event supervisor as last year. Last year's supervisor (who some of you may remember as kwijiborjt) wanted detail, detail, detail – chemically accurate, high-level creative additions. So that's how I built my model, with heteroatoms of relevant residues shown in CPK colors, and different colored thread corresponding to different types of bonds between residues, and so on. I tried to make my creative additions creative, with some more complex stuff in addition to the obvious additions, trying to show a deeper understanding of the protein's function. And I think some of it may have gone over the heads of the judges, who were probably judging the event for the first time and adhering exactly to the grading guidelines issued by MSOE. My more advanced creative additions wouldn't have been on the list of likely/suggested creative additions (which event supervisors are encouraged to look beyond at their own discretion), and may not have received any points. Similarly, my explanations for why the highlighted residues in the onsite were important (which came straight from the primary citation for 3OD8.pdb) may have been too technical and might not have gotten as many points as a more general explanation.

It's a shame – I think this is a better event when there's room to push your understanding farther – but at the same time, it's a good reminder that you should never rely too heavily on a particular supervisor's grading/writing style for your strategy in any event.

I can send you my state 3rd if you want. I don't think we could have gotten 3rd without your posts and contributions to the wiki. I can't wait to compete against you at nationals.