Protein Modeling C

User avatar
bernard
Administrator
Administrator
Posts: 1882
Joined: January 5th, 2014, 3:12 pm
Division: Grad
State: WA
Location: Seattle, WA
Contact:

Re: Protein Modeling C

Postby bernard » February 22nd, 2015, 10:17 pm

SAmoyo wrote:Is a pre-build of restriction endonuclease foki necessary for all levels of competition (regional, state, national)?

Yes.
"One of the ways that I believe people express their appreciation to the rest of humanity is to make something wonderful and put it out there."

SAmoyo
Member
Member
Posts: 3
Joined: February 22nd, 2015, 9:12 pm
State: -
Contact:

Re: Protein Modeling C

Postby SAmoyo » February 22nd, 2015, 10:52 pm

Thank you. And will it still be of amino acids 421-560?

User avatar
bernard
Administrator
Administrator
Posts: 1882
Joined: January 5th, 2014, 3:12 pm
Division: Grad
State: WA
Location: Seattle, WA
Contact:

Re: Protein Modeling C

Postby bernard » February 22nd, 2015, 10:59 pm

SAmoyo wrote:Thank you. And will it still be of amino acids 421-560?

I think so. I don't see anything in the rules that mentions it being different at different levels of competition.
"One of the ways that I believe people express their appreciation to the rest of humanity is to make something wonderful and put it out there."

User avatar
fozendog
Member
Member
Posts: 193
Joined: April 17th, 2012, 5:51 pm
Division: Grad
State: WA
Location: Camas
Contact:

Re: Protein Modeling C

Postby fozendog » February 23rd, 2015, 12:22 am

SAmoyo wrote:Is a pre-build of restriction endonuclease foki necessary for all levels of competition (regional, state, national)?

Gah, Bernard stays up late and answered it.
Stanford '19
Camas Science Olympiad Alumnus
Events: Protein Modeling, Cell Biology, Disease Detectives, Experimental Design, Dynamic Planet, Water Quality

User avatar
bernard
Administrator
Administrator
Posts: 1882
Joined: January 5th, 2014, 3:12 pm
Division: Grad
State: WA
Location: Seattle, WA
Contact:

Re: Protein Modeling C

Postby bernard » February 23rd, 2015, 12:23 am

fozendog wrote:
SAmoyo wrote:Is a pre-build of restriction endonuclease foki necessary for all levels of competition (regional, state, national)?

Gah, Bernard stays up late and answered it.

And Bernard stays up late and responds!
"One of the ways that I believe people express their appreciation to the rest of humanity is to make something wonderful and put it out there."

Chemchic
Member
Member
Posts: 3
Joined: January 4th, 2014, 11:56 pm
Division: C
State: MI
Contact:

Re: Protein Modeling C

Postby Chemchic » February 25th, 2015, 9:05 am

JonB wrote:
emmadej wrote:
bernard wrote:
Also, is there a way to get cheaper materials for the pre-build model than the 24$ one on the website?
I'd like to keep that snazzy tuber thing. c:


Here is an interesting material that we REALLY like to use for this event. It is sturdy, and fairly easy to work with:

http://www.niteize.com/product/Gear-Tie-64.asp

You will have to figure out how to connect several of them together to be long enough- but we really like them. They have them at Home Depot if you want to take a look at them. Is it collectively going to be cheaper than the Tubers? Well, the shipping from 3D molecular designs is really pricey, so if you purchase at Home Depot it might save some bucks.

I just ordered from Amazon. 2-32" (4 tot in pkgs) ties for ~11.50 (used free shping of Prime). Got the lime green and might use the lime green duct tape for the joins. I hated the shipping charges for a piddly, trashed, manila envelope from a few years ago...where 3D Molecular Designs charges $18 shipping and $28 for a single long toober!!!...so I refuse to buy from them. As long as items are properly marked, it shouldn't matter from what material the backbone is made.

JonB
Coach
Coach
Posts: 262
Joined: March 11th, 2014, 12:00 pm
Division: C
State: FL
Contact:

Re: Protein Modeling C

Postby JonB » February 25th, 2015, 9:34 am

Agreed. We have used these in all of our proteins. They look pretty good and are fairly easy to work with. They can be painted and glued fairly easily. If you have the capability, create 3D printed joints to connect them together (basically like a sleeve that both ends of the "protein" can slide into).

User avatar
bernard
Administrator
Administrator
Posts: 1882
Joined: January 5th, 2014, 3:12 pm
Division: Grad
State: WA
Location: Seattle, WA
Contact:

Re: Protein Modeling C

Postby bernard » February 25th, 2015, 9:47 am

JonB wrote:Agreed. We have used these in all of our proteins. They look pretty good and are fairly easy to work with. They can be painted and glued fairly easily. If you have the capability, create 3D printed joints to connect them together (basically like a sleeve that both ends of the "protein" can slide into).

Would you happen to know the name of the product Chemchic is referring to in this reply? I am thinking about getting some materials for our team to practice with for the onsite build. Do those materials work just like MiniToobers, which by my understanding are very commonly used for the onsite build?
"One of the ways that I believe people express their appreciation to the rest of humanity is to make something wonderful and put it out there."

JonB
Coach
Coach
Posts: 262
Joined: March 11th, 2014, 12:00 pm
Division: C
State: FL
Contact:

Re: Protein Modeling C

Postby JonB » February 25th, 2015, 10:28 am

bernard wrote:
JonB wrote:Agreed. We have used these in all of our proteins. They look pretty good and are fairly easy to work with. They can be painted and glued fairly easily. If you have the capability, create 3D printed joints to connect them together (basically like a sleeve that both ends of the "protein" can slide into).

Would you happen to know the name of the product Chemchic is referring to in this reply? I am thinking about getting some materials for our team to practice with for the onsite build. Do those materials work just like MiniToobers, which by my understanding are very commonly used for the onsite build?



http://www.niteize.com/product/Gear-Tie-64.asp

It would work well for practice.

User avatar
bernard
Administrator
Administrator
Posts: 1882
Joined: January 5th, 2014, 3:12 pm
Division: Grad
State: WA
Location: Seattle, WA
Contact:

Re: Protein Modeling C

Postby bernard » February 25th, 2015, 10:30 am

JonB wrote:
bernard wrote:
JonB wrote:Agreed. We have used these in all of our proteins. They look pretty good and are fairly easy to work with. They can be painted and glued fairly easily. If you have the capability, create 3D printed joints to connect them together (basically like a sleeve that both ends of the "protein" can slide into).

Would you happen to know the name of the product Chemchic is referring to in this reply? I am thinking about getting some materials for our team to practice with for the onsite build. Do those materials work just like MiniToobers, which by my understanding are very commonly used for the onsite build?



http://www.niteize.com/product/Gear-Tie-64.asp

It would work well for practice.

Are they as rigid as copper wire or MiniToobers? Can they be written on with permanent marker?
"One of the ways that I believe people express their appreciation to the rest of humanity is to make something wonderful and put it out there."

JonB
Coach
Coach
Posts: 262
Joined: March 11th, 2014, 12:00 pm
Division: C
State: FL
Contact:

Re: Protein Modeling C

Postby JonB » February 25th, 2015, 11:12 am

I would say just about as rigid as copper wire, maybe a little less. It can be written on with permanent marker (some might rub off).

User avatar
bernard
Administrator
Administrator
Posts: 1882
Joined: January 5th, 2014, 3:12 pm
Division: Grad
State: WA
Location: Seattle, WA
Contact:

Re: Protein Modeling C

Postby bernard » February 25th, 2015, 2:12 pm

JonB wrote:I would say just about as rigid as copper wire, maybe a little less. It can be written on with permanent marker (some might rub off).

That sounds perfect! I've used copper wire and it can take quite some movement without deforming, which has happened to our MiniToobers occasionally. Thanks for the help!
"One of the ways that I believe people express their appreciation to the rest of humanity is to make something wonderful and put it out there."

tylarthefarmer
Member
Member
Posts: 2
Joined: October 6th, 2014, 11:47 am
State: -
Contact:

Re: Protein Modeling C

Postby tylarthefarmer » February 25th, 2015, 8:50 pm

annaphase wrote:
tylarthefarmer wrote:Hi guys,
If I wanted to model the DNA-binding domain of the FokI protein for use as a creative addition, what amino acid sequence would I isolate in Jmol in order to model said domain?

Ahaha I'll give you a hint: it's out there. Read journal articles, read databases, and you will find everything you need to know. Trust me, a few weeks ago I was banging my head on the wall because, as far as I could tell, no one gave a **** about the protein and there was no information on it but when you do the research and when you find it all out it's really, really awesome. Use the protein modeling website from the event sponsor, and they have all the information about the different domains, but it's no fun if you don't do the research yourself :) It's not hard to find, I promise. A carefully worded google search and some patience will do the trick.



Thank you! Just knowing the information exists is all I needed!

Dhruvster
Member
Member
Posts: 30
Joined: June 7th, 2014, 10:10 pm
Division: Grad
State: TX
Contact:

Re: Protein Modeling C

Postby Dhruvster » March 2nd, 2015, 7:14 am

Hey I had two questions
Has anyone who has done this event at nats know the time constraints that they give us there. Like the whole 50 min for both the test/onsite or are they split.
Also does anyone know how much the creative additions are actually worth. I've been to tournaments where they are 4/40 and other where they are about 16 out of 40, and the nationals rubric from 2012 has them being about 16/40? I can't seem to find a clear answer on this.
Thanks!

alwaysfaith
Member
Member
Posts: 3
Joined: March 2nd, 2015, 5:39 pm
State: -
Contact:

Re: Protein Modeling C

Postby alwaysfaith » March 2nd, 2015, 6:03 pm

It's 50 min. for all onsite (building & protein). It's not 50 min. for the test and another 50 min. for the onsite build. Each addition is 4 points and you can get a max of 16 extra points.


Return to “2015 Lab Events”

Who is online

Users browsing this forum: No registered users and 1 guest