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Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains


Amino acids have sidechain rotamer preferences dependent on the backbone dihedral angles φ and ψ. These preferences provide a method for rapid structure prediction which is a significant improvement over backbone-independent rotamer libraries. We demonstrate here that simple arguments based on conformational analysis can account for many of the features of the observed backbone dependence of the sidechain rotamers. Steric repulsions corresponding to the ‘butane’ and ‘syn-pentane’ effects make certain conformers rare, as has been observed experimentally.

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Dunbrack, R., Karplus, M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nat Struct Mol Biol 1, 334–340 (1994).

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