Rotamers

Dead-end Elimination - Protein Design
... The preceding discussion implicitly assumed that the rotamers are all different orientations of the same amino acid side chain ... to "compete" over a position by including both types of side chains in the set of rotamers for that position ... However, this greatly increases the number of rotamers per position and still requires a fixed protein length ...

Dead-end Elimination - Applications To Protein Structure Prediction
... The dihedral angle search space of the side chains is restricted to a discrete set of rotamers for each amino acid position in the protein (which is, obviously, of fixed ... criteria for the elimination of single rotamers and of rotamer pairs, although this can be expanded ... In the following discussion, let be the length of the protein and let represent the rotamer of the side chain ...

Self-consistent Mean Field (biology) - General Principles
... dihedral angles of each side chain into a set of rotamers for each position in the protein sequence ... description of the relative population of each possible rotamer at each position, and the probability of a given structure is defined as a function ... distribution describing the starting population of each individual rotamer A way of updating rotamer energies and probabilities as a function of the mean-field energy The process is ...

Protein Structure Prediction - Tertiary Structure - Side-chain Geometry Prediction
... on the rigid polypeptide backbone and using a set of discrete side chain conformations known as "rotamers." The methods attempt to identify the set of ... These methods use rotamer libraries, which are collections of favorable conformations for each residue type in proteins ... Rotamer libraries may contain information about the conformation, its frequency, and the standard deviations about mean dihedral angles, which can be used in sampling ...