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?
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.
The I-Tasser web server from Zhang lab could also do the job.
Apart from modeller, you can use Swiss model,Phyre ,these are web based servers to model protein.
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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version 2.3.6
Here is the website: http://salilab.org/modeller/ And here is a good tutorial to start with: http://salilab.org/modeller/tutorial/basic.html
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.
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?