Question: Fixing Amino Acid Residues In Disallowed Region
1
gravatar for Tofayel Ahmed
5.8 years ago by
India
Tofayel Ahmed40 wrote:

My modelled protein contains 8 residues in disallowed region. what can I do to fix those? somebody told me to generate rotamers for the side chains in Swiss PDBViewer; other person suggested to go for energy minimization doing MD. any suggestions on this?

protein • 1.3k views
ADD COMMENTlink written 5.8 years ago by Tofayel Ahmed40
1
gravatar for Istvan Albert
5.8 years ago by
Istvan Albert ♦♦ 73k
University Park, USA
Istvan Albert ♦♦ 73k wrote:

via Khader Shameer --> see also: http://biostar.stackexchange.com/questions/4661/structural-bioinformatics-approaches-to-fix-residues-in-dis-allowed-regions-of-ra

ADD COMMENTlink written 5.8 years ago by Istvan Albert ♦♦ 73k

Thank you Dr. Albert. The link sent by you answers it all.

ADD REPLYlink written 5.8 years ago by Tofayel Ahmed40
0
gravatar for ALchEmiXt
5.8 years ago by
ALchEmiXt1.8k
The Netherlands
ALchEmiXt1.8k wrote:

Did the model come from homolgy-modelling or did you build it somewhere else from other/lab data? Anyway, give DeepView Swiss PDBviewer a go. It can minimize threaded not too complex structures quite well.

ADD COMMENTlink written 5.8 years ago by ALchEmiXt1.8k

Thank you Dr. Albert. The link sent by you answers it all.

ADD REPLYlink written 5.8 years ago by Tofayel Ahmed40

Thanks for your concern. It is built by me via homology modeling. would definitely give a try in deepview.

ADD REPLYlink written 5.8 years ago by Tofayel Ahmed40
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