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I have multiple X-ray structures (PDB files) of the same protein. All of them have missing stretches of residues. I want to use all of them to build a single model, with as little missing residues as possible. Is there a tool (web-server, software) available to do this?

In a particular application, I have one additional requirement. One of the PDB files is special (call it the template), in the sense that I only want to add missing residues to it. That is, the resulting model should contain the special pdb file, and align perfectly to it, the only difference being that the resulting model has some additional residues that were completed from the information in the other pdb files. Okay, the resulting model should not align "perfectly" to the template. I'll allow some relaxation in the connecting points. But still, the idea is that the template PDB should carry a "larger weight".

So, those are the two problems: 1) How to reconstruct a more complete model from a bunch of PDB files of the same protein? 2) How to complete missing residues in one PDB file using information from other PDB files of the same protein?

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  • $\begingroup$ I'm not an expert on this, but the technical term you're looking for is "loop modeling", e.g. en.wikipedia.org/wiki/Loop_modeling -- I hope this gives you some leads $\endgroup$
    – Michael Kuhn
    Commented Aug 24, 2015 at 8:30
  • $\begingroup$ @MichaelKuhn That's the appropriate term if the missing residues are located on a loop (which they usually are). $\endgroup$
    – a06e
    Commented Aug 24, 2015 at 12:14

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I suggest you to use modeller - advance modelling (https://salilab.org/modeller/tutorial/advanced.html), Where you can use multiple template PDB to get final model structure.

All the best..:)

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    $\begingroup$ Please add some explanation. This looks more like a comment. $\endgroup$
    – WYSIWYG
    Commented Jan 9, 2017 at 6:01

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