Question: Is There A Web Based Tool For Fixing Pdb Protein Structures That May Have Missing Atoms?
1
gravatar for Flow
6.7 years ago by
Flow1.5k
Flow1.5k wrote:

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 • 6.6k views
ADD COMMENTlink modified 6.7 years ago by quentin.delettre430 • written 6.7 years ago by Flow1.5k

http://www.ebi.ac.uk/pdbsum/ might be useful for you.

ADD REPLYlink written 6.7 years ago by aravind ramesh510

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

ADD REPLYlink written 6.7 years ago by Flow1.5k
0
gravatar for João Rodrigues
6.7 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

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).

ADD COMMENTlink written 6.7 years ago by João Rodrigues2.5k
0
gravatar for quentin.delettre
6.7 years ago by
France
quentin.delettre430 wrote:

Construct missing side chains from PDB file

Another biostar thread about missing things

Or as previously mentionned, Modeller.

ADD COMMENTlink written 6.7 years ago by quentin.delettre430

thanks but second link does not worl

ADD REPLYlink written 6.7 years ago by Flow1.5k

Strange. Here it is : Adding missing atoms to PDB

ADD REPLYlink written 6.7 years ago by quentin.delettre430
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