Rotamers state in protein design

Question

[alvieirajr]

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.

Answer 1

[João Rodrigues]

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.

[alvieirajr]

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 ?

[João Rodrigues]

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.