Protein Structure Reconstruction
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9.6 years ago
Plasmid ▴ 160

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 • 3.0k views
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9.6 years ago
dimkal ▴ 730

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.

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

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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.

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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?

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9.6 years ago

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

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

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9.6 years ago
Zak ▴ 110

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

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

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9.6 years ago
João Rodrigues ★ 2.5k

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.

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