Using quantum mechanics to improve estimates of amino acid side chain rotamer energies.

ABSTRACT: Amino acid side chains adopt a discrete set of favorable conformations typically referred to as rotamers. The relative energies of rotamers partially determine which side chain conformations are more often observed in protein structures and accurate estimates of these energies are important for predicting protein structure and designing new proteins. Protein modelers typically calculate side chain rotamer energies by using molecular mechanics (MM) potentials or by converting rotamer probabilities from the protein database (PDB) into relative free energies. One limitation of the knowledge-based energies is that rotamer preferences observed in the PDB can reflect internal side chain energies as well as longer-range interactions with the rest of the protein. Here, we test an alternative appro

SUBMITTER: Renfrew PD 

PROVIDER: S-EPMC2680024 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature