Question

Fixing Amino Acid Residues In Disallowed Region

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12.6 years ago

Tofayel Ahmed ▴ 40

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 • 2.7k views

ADD COMMENT • link updated 12.6 years ago by Istvan Albert 100k • written 12.6 years ago by Tofayel Ahmed ▴ 40

Ram · Answer 1 · 2011-09-23

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12.6 years ago

Istvan Albert 100k

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

ADD COMMENT • link updated 4.6 years ago by Ram 43k • written 12.6 years ago by Istvan Albert 100k

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

ADD REPLY • link 12.6 years ago by Tofayel Ahmed ▴ 40

score 0 · Answer 2 · 2011-09-22

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12.6 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.

ADD COMMENT • link 12.6 years ago by ALchEmiXt ★ 1.9k

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

ADD REPLY • link 12.6 years ago by Tofayel Ahmed ▴ 40

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

ADD REPLY • link 12.6 years ago by Tofayel Ahmed ▴ 40