Protein Modeling C

ericlepanda
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Re: Protein Modeling C

Postby ericlepanda » November 21st, 2018, 3:45 pm

Wait how do we figure out the amino acid sequence of the Anti-Crispr
you can find the sequences for both the anti-crispr and the cas-9 on rcsb
http://www.rcsb.org/pdb/explore/remedia ... ureId=5VW1
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PeptoBismol
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Re: Protein Modeling C

Postby PeptoBismol » November 22nd, 2018, 12:48 pm

With 5vw1, I restricted it to the b chain only and found that, when I restricted it to 1-60 through 1-85 nothing happened, but when I restricted it to 1-59, some of the chain was removed, which makes me believe the b chain is 60 residues long. But I know it is at least 85 long, so how does this work out? Am I doing something wrong, or does the build contain both a and b?

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Re: Protein Modeling C

Postby JoeyC » November 22nd, 2018, 1:09 pm

restrict 1-85
restrict :b
If the chain does not have 3 Alpha Helices and 3 Beta Pleated Sheets, your program is recognizing the wrong chain.
It should look as such: https://drive.google.com/file/d/1UQgeeS ... sp=sharing
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Re: Protein Modeling C

Postby greenMountainCoffee » November 25th, 2018, 3:29 pm

Hi,
This may be a stupid question, but on the JSMOL thing, it says the protein we should build is 84 residues long. Does that mean we should include residue #1 and include residue #84?

Sorry this was worded weirdly too

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Re: Protein Modeling C

Postby Limke » November 25th, 2018, 3:31 pm

Hi,
This may be a stupid question, but on the JSMOL thing, it says the protein we should build is 84 residues long. Does that mean we should include residue #1 and include residue #84?

Sorry this was worded weirdly too
Yes, include residue 1 and 85*.
Also, just a clarification, the rules say to build residues 1-85.
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Re: Protein Modeling C

Postby RishiVanga » November 26th, 2018, 5:31 am

So I don't know if I'm just searching it wrong but I can't seem to find a place to buy Mini Toobers for modeling the structure. Could someone send me a link to where I can buy them?

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Re: Protein Modeling C

Postby MyWorldRules » November 26th, 2018, 5:49 am

Can someone please send us their files containing their work. I am really confused and would like to reference of someone. Thx x

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Re: Protein Modeling C

Postby greenMountainCoffee » November 26th, 2018, 8:04 am

Hi,
This may be a stupid question, but on the JSMOL thing, it says the protein we should build is 84 residues long. Does that mean we should include residue #1 and include residue #84?

Sorry this was worded weirdly too
Yes, include residue 1 and 85*.
Also, just a clarification, the rules say to build residues 1-85.
Right but then... the protein would be 85 residues right?

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Re: Protein Modeling C

Postby meierfra » November 26th, 2018, 10:14 am

So I don't know if I'm just searching it wrong but I can't seem to find a place to buy Mini Toobers for modeling the structure. Could someone send me a link to where I can buy them?
This https://www.3dmoleculardesigns.com/Scie ... g-Kits.htm is the site to buy a Mini Toober for the Pre-Build. You can also buy a practice kit that was the 2016 Regional On-site. This is the information page; click the blue "Buy Now" button to take you to a shopping page.

You know you don't have to buy the Mini Toobers. Less expensive options include 12 guage wire and this foam wire https://www.amazon.com/dp/B0026WGDYW/?c ... _lig_dp_it that Andy Hamm suggested to me. (It says size 12, but you just get one 32' roll.)

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Re: Protein Modeling C

Postby pikachu4919 » November 26th, 2018, 2:55 pm

So I don't know if I'm just searching it wrong but I can't seem to find a place to buy Mini Toobers for modeling the structure. Could someone send me a link to where I can buy them?
This https://www.3dmoleculardesigns.com/Scie ... g-Kits.htm is the site to buy a Mini Toober for the Pre-Build. You can also buy a practice kit that was the 2016 Regional On-site. This is the information page; click the blue "Buy Now" button to take you to a shopping page.

You know you don't have to buy the Mini Toobers. Less expensive options include 12 guage wire and this foam wire https://www.amazon.com/dp/B0026WGDYW/?c ... _lig_dp_it that Andy Hamm suggested to me. (It says size 12, but you just get one 32' roll.)
I would say that from an objective standpoint, the main advantage with buying the kits to build with would be that everything is cut to the exact length that the model needs to be, as well as the fact that it provides some supports and caps for the N and C termini, and the onsite practice kits also have model amino acid parts as well (although that's not necessarily the most efficient way to get amino acid residues, you can easily make them out of whatever material your heart desires within the scope of the rules).

It's more or less a convenience thing, if anything. I know plenty of models have been really good and high-scoring without using the kits as well. Totally up to you.
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