Question: Protein Structure Reconstruction
2
gravatar for Plasmid
8.7 years ago by
Plasmid160
European Union
Plasmid160 wrote:

I am new to protein structure reconstruction. Can anyone help to find a best program or tools to reconstruct 3D structure of a part of protein that portion is missing in PDB?

protein modeling homology • 2.8k views
ADD COMMENTlink modified 4.9 years ago by Biostar ♦♦ 20 • written 8.7 years ago by Plasmid160
4
gravatar for dimkal
8.7 years ago by
dimkal730
United States
dimkal730 wrote:

Try a program called "Modeller" from Sali's lab, which lets you model missing parts of the system. The program is free to academics and has a tutorial but it's mostly driven by running python scripts through the command line. If you're looking for more graphic-friendly approach look into Prime by Schrodinger. This program is not free, but i'm sure you can get an evaluation copy to try it out.

ADD COMMENTlink written 8.7 years ago by dimkal730

Here is the website: http://salilab.org/modeller/ And here is a good tutorial to start with: http://salilab.org/modeller/tutorial/basic.html

ADD REPLYlink written 8.7 years ago by Keith Callenberg900

Modeller is litte bit complicated to use. I tried to use graphic interface like Pymod and Chimera. But it still trying to get good result. I didn't found any price information in Prime's website. How much it costs? Thanks for your help.

ADD REPLYlink written 8.7 years ago by Plasmid160

i'm not sure about prime's pricing, but i know it's very expensive. Maybe your institution already has access to it, ask around. how big of a fragment are you trying to reconstruct?

ADD REPLYlink written 8.7 years ago by dimkal730
1
gravatar for Pierre Poulain
8.7 years ago by
France
Pierre Poulain440 wrote:

The I-Tasser web server from Zhang lab could also do the job.

ADD COMMENTlink written 8.7 years ago by Pierre Poulain440

I used it several years ago. Now again I used it. It's amazing a lot of update happened since I used. Thanks.

ADD REPLYlink written 8.7 years ago by Plasmid160
0
gravatar for Zak
8.7 years ago by
Zak110
Zak110 wrote:

Apart from modeller, you can use Swiss model,Phyre ,these are web based servers to model protein.

ADD COMMENTlink written 8.7 years ago by Zak110

I used the phyre but the out put is only nearest PDB protein not whole protein. Thanks for reply.

ADD REPLYlink written 8.7 years ago by Plasmid160
0
gravatar for João Rodrigues
8.7 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

If you just want to rebuild part of a protein, say, side chains, have a look at the WHATIF servers. If you want to model part of a protein, indeed use Phyre, Swiss-Model, or MODELLER. MODELLER might seem hard in the beginning but you will learn a lot from using it and it is in fact pretty straightforward for simple cases, they have pretty much "pre-built" scripts ready for you to download and use, you just need an alignment.

ADD COMMENTlink written 8.7 years ago by João Rodrigues2.5k
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