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Is There A Web Based Tool For Fixing Pdb Protein Structures That May Have Missing Atoms?

Some protein files from PDB database have missing atoms, so when I use them with some molecular modeling programs, they complain about it. Is it there any web server that can fix/heal them? SOmebody told me about MODELLER, but as far as I know they do not have a server.

protein structure
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updated by quentin.delettre quentin.delettre • written by Flow Flow

thanks, but that is just a database, I do not see how that could fix the protein !

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written by Flow Flow

2 answers

Hi,

Use this interface for MODELLER, you should be able to upload your template (your incomplete protein structure) and paste the sequence alignment between your sequence and your protein (essentially, the same sequence repeated twice).

The only thing you need is the MODELLER key, which you can get in the MODELLER website upon registration for a license (for free).

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written by João Rodrigues João Rodrigues

Construct missing side chains from PDB file

Another biostar thread about missing things

Or as previously mentionned, Modeller.

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written by quentin.delettre quentin.delettre

thanks but second link does not worl

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written by Flow Flow

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