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Fixing Amino Acid Residues In Disallowed Region

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
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updated by Istvan Albert Istvan Albert • written by Tofayel Ahmed • Tofayel Ahmed

2 answers

via Khader Shameer --> see also: https://biostars.org/p/4653/

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updated by Ram Ram • written by Istvan Albert Istvan Albert

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

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written by Tofayel Ahmed • Tofayel Ahmed

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.

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written by ALchEmiXt ALchEmiXt

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

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written by Tofayel Ahmed • Tofayel Ahmed

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

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written by Tofayel Ahmed • Tofayel Ahmed

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