Help on job https://mobyle.rpbs.univ-paris-diderot.fr/data/jobs/DaReUS-Loop/C22356007522106

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Hello. I wish to refine the loops of my protein structure which I generated by homology modelling. Neither my Sequence, nor the PDB structure file has any gaps. What can I do in this case?

Awaiting your reply!

REGARDS
Asif Shuvro

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  • id: V15585232508898
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Hello Asif,

In that case, upload the full PDB, but you must upload your own gapped sequence. With the gaps, you indicate the loop regions to be remodeled.

In general, best results are obtained if a (re)modeled loop is flanked by helices or strands. If this is not the case, you might consider to extend the loop region towards the nearest helix or strand.

cheers

Sjoerd

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