Protein Modeling C

meierfra
Member
Member
Posts: 55
Joined: August 23rd, 2016, 10:01 am
Division: C
State: MI

Re: Protein Modeling C

Postby meierfra » November 18th, 2018, 12:00 pm

How can you convert the mess of 4un3 to something that doesn't give me a stroke when you look at it?

Any links to tutorials would be nice too thanks.
The MSOE website has a bunch of tutorials on how to use Jmol and restrict domains (removing all the residues you don't need, showing certain sidechains, restricting to just the backbone (2ndary structure)

http://cbm.msoe.edu/scienceOlympiad/participant3.php

Scroll down on that page and they should have links under their Advanced Jmol training guide, which I found particularly helpful!
Thank you so much!
You realize that for the Pre-build there's a Rules Clarification and we're supposed to do 5vw1, right?

rhkoulen
Member
Member
Posts: 5
Joined: April 15th, 2015, 1:16 pm

Re: Protein Modeling C

Postby rhkoulen » November 18th, 2018, 4:11 pm

Dude, I like, uhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh just did the whole dam thang for 4un3 so like


: D

KSSOISLIT
Member
Member
Posts: 15
Joined: April 18th, 2016, 10:03 am
Division: C
State: KS

Re: Protein Modeling C

Postby KSSOISLIT » November 19th, 2018, 2:15 pm

Does anyone here know what specific criteria judges use to grade the pre-build? I.e. a rubric? I understand how they grade for basic structure stuff, but how do they designate different point values for the creative additions? Thanks...
Olathe North High School
[b]Past Events:[/b] Anatomy, Bridges, Crime Busters, ELG, Helicopters, Mission Possible, Towers
[b]2019 Events:[/b] Boom, Fermi, Forensics, Protein, Wright Stuff

User avatar
pikachu4919
Moderator
Moderator
Posts: 685
Joined: December 7th, 2012, 2:30 pm
Division: Grad
State: IN
Location: West [Favorite Fightin' Frenchman!]

Re: Protein Modeling C

Postby pikachu4919 » November 19th, 2018, 2:38 pm

Does anyone here know what specific criteria judges use to grade the pre-build? I.e. a rubric? I understand how they grade for basic structure stuff, but how do they designate different point values for the creative additions? Thanks...
There is a rubric, but I believe it's usually only given to event supervisors.
Carmel HS (IN) '16
Purdue BiolE '20
Nationals 2016 ~ 4th place Forensics


Not throwin' away my shot!
MY CABBAGES!

pikachu4919's Userpage

Opinions expressed on this site are not official; the only place for official rules changes and FAQs is soinc.org.

Rate my tests!

labgirl
Member
Member
Posts: 1
Joined: November 19th, 2018, 3:38 pm

Re: Protein Modeling C

Postby labgirl » November 19th, 2018, 3:47 pm

Hey guys!

Just a clarification (because it's not specified on the rules) the residues 1-85 refers to those on the B chain, correct? It's the only chain actually labeled "Anti-CRISPR protein," but I'd like confirmation before I show up to competition with the wrong chain. XP

Also, does anyone have any tips for finding what "functionally relevant features" to note on the model? I did this as a trial event last year, and trying to figure out what to mark was the thing my partner and I struggled with the most.

Thanks! :)

User avatar
pikachu4919
Moderator
Moderator
Posts: 685
Joined: December 7th, 2012, 2:30 pm
Division: Grad
State: IN
Location: West [Favorite Fightin' Frenchman!]

Re: Protein Modeling C

Postby pikachu4919 » November 19th, 2018, 4:36 pm

Hey guys!

Just a clarification (because it's not specified on the rules) the residues 1-85 refers to those on the B chain, correct? It's the only chain actually labeled "Anti-CRISPR protein," but I'd like confirmation before I show up to competition with the wrong chain. XP

Also, does anyone have any tips for finding what "functionally relevant features" to note on the model? I did this as a trial event last year, and trying to figure out what to mark was the thing my partner and I struggled with the most.

Thanks! :)
To the first question, I believe so. After playing around with it in the JSmol on CBM's website, it appears that the 5vw1.pdb file contains an A and a B chain, however, after manipulating a handful of things in the environment, it appears that the B chain seems to be 85 residues long (not counting residue 0, which exists in this pdb file) and is completely detached from the A chain (which is many more amino acids long yet still has a 1-85 as well). However, the provided JSmol design environment on the official website for protein modeling does say B chain in its prebuild visualization environment, which is why you could reasonably suspect that the prebuild is that way. If you really, really want to make sure, you could submit a FAQ or clarification to the National Committee here if you feel like it.

In terms of the bonus "functionally relevant features" part, my best recommendation is to read the paper that the protein is based off of to determine those. The paper will give you plenty of ideas by mentioning several different very crucial amino acids, ligands, or any other things critical to the protein function. Then it's up to you to decide which ones you would want to portray, if any, and how you want to do that.
Carmel HS (IN) '16
Purdue BiolE '20
Nationals 2016 ~ 4th place Forensics


Not throwin' away my shot!
MY CABBAGES!

pikachu4919's Userpage

Opinions expressed on this site are not official; the only place for official rules changes and FAQs is soinc.org.

Rate my tests!

User avatar
EastStroudsburg13
Administrator
Administrator
Posts: 3035
Joined: January 17th, 2009, 7:32 am
Division: Grad
State: MD
Location: At work trying to be a real adult
Contact:

Re: Protein Modeling C

Postby EastStroudsburg13 » November 20th, 2018, 6:37 am

Does anyone here know what specific criteria judges use to grade the pre-build? I.e. a rubric? I understand how they grade for basic structure stuff, but how do they designate different point values for the creative additions? Thanks...
There is a rubric, but I believe it's usually only given to event supervisors.
Also, from what I recall, the rubric differs depending on the level of competition. The state and national rubrics had progressively higher standards to earn points, especially for the additions.
East Stroudsburg South Class of 2012, Alumnus of JT Lambert, Drexel University Class of 2017

Helpful Links
Wiki
Wiki Pages that Need Work
FAQ and SciOly FAQ Wiki
Chat (See IRC Wiki for more info)
BBCode Wiki


So long, and thanks for all the Future Dictator titles!

User avatar
platypusomelette
Member
Member
Posts: 79
Joined: May 7th, 2017, 2:41 pm
Division: C
State: NY
Location: biology

Re: Protein Modeling C

Postby platypusomelette » November 20th, 2018, 7:18 am

Does anyone here know what specific criteria judges use to grade the pre-build? I.e. a rubric? I understand how they grade for basic structure stuff, but how do they designate different point values for the creative additions? Thanks...
There is a rubric, but I believe it's usually only given to event supervisors.
Also, from what I recall, the rubric differs depending on the level of competition. The state and national rubrics had progressively higher standards to earn points, especially for the additions.
Wait do you know where to find sample rubrics?
island trash trees hs
anat: reg 4th
herp: reg 6th
genes: reg 5th
protein: reg 2nd
disease: reg 15th
fossils: reg 4th
2016: a&p 1st, fossils 3rd
2017: a&p 3rd, herp 14th
2018: a&p 1st, microbe 8th, herp 13th :/
HELL YEA WE MADE STATES

User avatar
EastStroudsburg13
Administrator
Administrator
Posts: 3035
Joined: January 17th, 2009, 7:32 am
Division: Grad
State: MD
Location: At work trying to be a real adult
Contact:

Re: Protein Modeling C

Postby EastStroudsburg13 » November 20th, 2018, 7:29 am


There is a rubric, but I believe it's usually only given to event supervisors.
Also, from what I recall, the rubric differs depending on the level of competition. The state and national rubrics had progressively higher standards to earn points, especially for the additions.
Wait do you know where to find sample rubrics?
I don't think there is any central repository, but the wiki has two examples from past national tournaments linked to in its description of the on-site model.
East Stroudsburg South Class of 2012, Alumnus of JT Lambert, Drexel University Class of 2017

Helpful Links
Wiki
Wiki Pages that Need Work
FAQ and SciOly FAQ Wiki
Chat (See IRC Wiki for more info)
BBCode Wiki


So long, and thanks for all the Future Dictator titles!

aaaaaa
Member
Member
Posts: 1
Joined: November 21st, 2018, 2:42 pm

Re: Protein Modeling C

Postby aaaaaa » November 21st, 2018, 2:44 pm

Wait how do we figure out the amino acid sequence of the Anti-Crispr


Return to “2019 Lab Events”

Who is online

Users browsing this forum: No registered users and 2 guests