3D Analysis :: Rotamers
Rotamers are usually defined as low energy side-chain conformations. The use of a build-library of rotamers allows anyone determining or modeling a structure to try the most likely side-chain conformations, saving time and producing a structure that is more likely to be correct. This is, of course, only the case if the rotamers really are the correct low energy conformations. Our libraries address this quality issue in a number of ways:
We have two rotamer collections to offer: 1) the Penultimate Rotamer Library and 2) (son of) Penultimate Rotamer Library. These datasets are not only different in the underlying datasources, but they are also different in the presentation and use of the results. The Penultimate Rotamer Library results are presented as tables of confomers with geometries as specified by modal values of the residues diherals. Thus, one possible use of it is as a build library for model fitting. (son of) Penultimate Rotamer Library is a working dataset contoured by a density-dependent function as used for our Ramachandran boundaries update. You won't find tables of declared rotamers, rather, you'll be able to query the "rotamericity" of a point in dihedral space. It is used this way in our MolProbity web service to flag "bad rotamers" in structure models.
Also on this page, you'll find links to software packages which use one of our libraries. (If you know of any others, then please let us know!) Finally, we also link rotamer collections done by other labs; again, if you know of others, then please let us know.
(son of) Penultimate Rotamer Library
The database of structures supporting this library is our top500 database. Phi/psi dihedrals of this database were used in our Ramachandran update and some of the methods discussed in that publication (linked below) are germane to the rotamer product. Additionally, the README file, which is also part of the download package, goes into detail as to the methods used.
Penultimate Rotamer Library
The database of structures supporting this library is our : top240.pdf (40KB).
These two rotamer datasets are used in several software packages:
Backbone dependent Library for Asp and Asn
Our analysis suggests that for most residues the backbone conformation changes the frequency of the rotamers but not their position. The frequencies for each secondary structural class are given in the above files. However, for two amino acids, Asp and Asn, the positions also change with backbone secondary structure. Here is the breakout for Asp and Asn: bbdep_table.pdf (40KB)
Other rotamer libraries available on the web