Rotamer position specific

Figure 2 Position-specific rotamer distributions for Phe, His, and Tyr at the second and...

Chinea, Vriend [194, 284] WHAT IF Position specific rotamers extracted from PDB, 5-7 aa Packing + HB + vdw... 

G. Chinea, G. Padron, R. W. Hooft, C. Sander, G. Vriend. The use of position-specific rotamers in model building by homology. Proteins. 1995, 23, 415-421. 

The latest developments in modeling are position-specific rotamer searches (Fig. 2). Dunbrack et al. and Vriend et al. showed that the preferred rotamer is to a large extent determined by a local backbone [34,35], Database searches for peptides with the same local backbone and the same amino acid type in the middle often reveal a more restricted pattern of side-chain conformations than one would expect from generalized rotamer libraries. Position-specific rotamer distributions are obtained by searching the database for segments of residues that fulfill two criteria ... 

Figure 2 Position-specific rotamer distributions for Phe, His, and Tyr at the second and penultimate position in a short a-helix. It can be seen that only one rotamer is allowed at the C-terminal end, whereas the rotamer distribution is residue dependent at the N-terminal end of the helix. These rotamer distributions are obtained by searching the protein structure database for segments of residues that fulfill two criteria (1) the segment has a local backbone conformation similar to that of the fragment around the residue that has to be modeled, and (2) the database segment has the residue type at the middle position that has to be modeled.

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