Rotamers state in protein design
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7.5 years ago
alvieirajr • 0

Hi folks! Why we use the side-chain rotamers state in protein design? If after synthesis of protein I don't know if the residues will assume the rotamers state with was used.

protein-design aminoacid rotamer • 1.3k views
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7.5 years ago
João Rodrigues ★ 2.5k

Hi,

It was observed (and calculated) that side chains tend to adopt preferential orientations in protein structures. Therefore, instead of brute-forcing a conformational space search, it is simpler to just iterate over a list of preferred orientations.

Simplicity and efficiency. Otherwise protein design could take much much longer.

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Hi João! Thanks for reply.

So, don't you use the rotamers, right? thinking in this form ... how i can identify this preferential orientations ? Exist this protocol in literature ?

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I justified the use of rotamer libraries. Sorry if I wasn't clear. These preferential orientations are the rotamers. Look for papers of Roland Dunbrack.

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