completing incomplete PDBs

[Christoph Nimptsch <christoph.nimptsch AT uni-tuebingen.de>]

Hi,

assume, I have a PDB file template with some residues missing, e.g. 5 Amino 
acids at the beginning, 10 in the middle and 2 at the end of the sequence.

Now, I use Modeller to complete the template (I align the PDB to its 
sequence) and use it for homology modelling.

Is this a common procedure? What do you think about it? Will the completed 
template be reliable or should I leave the gaps of the template unfixed in 
homology modelling?

Thanks in advance,

Christoph Nimptsch




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Christoph Nimptsch
Apotheker
Pharmazeutisches Institut
Arbeitskreis Prof. Kovar
Universität Tübingen
Auf der Morgenstelle 8
D-72076 Tuebingen
Tel.: 07071 / 29 73047
Fax.: 07071 / 29 2470
mailto:christoph.nimptsch AT uni-tuebingen.de
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