Fixing Amino Acid Residues In Disallowed Region
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9.6 years ago

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?

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9.6 years ago

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

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

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9.6 years ago
ALchEmiXt ★ 1.9k

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

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

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