Phe rotamers

Phe rotamers of the Penultimate Rotamer Library

34 Arg rotamers

Arg rotamers at 1% level of (son of) Penultimate Rotamer Library

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 use only very high resolution structures (1.8 Å or better),
  • we remove side chains whose position may be in doubt using a number of filters,
  • we use the mode rather than the mean of observed conformations (which has a number of advantages), and
  • we make efforts to remove systematically misfit conformations.

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.

 (80MB)
top500-angles.050606.zip
The library archive.
 (788KB)
2003LovellPsfg50.pdf
Publication/citation on Ramachandran update use of the library:
S.C. Lovell, I.W. Davis, W.B. Arendall III, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, and D.C. Richardson (2003) "Structure Validation by Cα Geometry: φ,ψ and Cβ Deviation" Proteins: Structure, Function and Genetics 50: 437-450.

Penultimate Rotamer Library

The database of structures supporting this library is our : download arrow top240.pdf (40KB).

 (296KB)
2000LovellPsfg40.pdf
Publication/citation on Penultimate Rotamer Library
SC Lovell, JM Word, JS Richardson and DC Richardson (2000) "The Penultimate Rotamer Library" Proteins: Structure Function and Genetics 40: 389-408.
 (20KB)
rotpapertable1.pdf
The library as it appears in the publication.
 (24KB)
Complete_rotamer_lib.pdf
A fuller description, with assymetric widths and explicit bins.
 (20KB)
RotTabSuggestedUse.pdf
A version for use in automated procedures, with common-atom angles and samples.

Software

These two rotamer datasets are used in several software packages:

  • O -- this popular model building software has two database files built with the Penultimate Rotamer Library's common-atom angles. See our web page, Rotamers for O, for details and download links
  • Xtalview -- also has a library for our rotamers, see the page, Rotamers for Xtalview, for details and download links.
  • MolProbity -- our web service for structural model quality uses the (son of) Penultimate Library in its assessment of rotamer quality.
  • KiNG & mage -- our two kinemage display programs both use our rotamers in their build/mutate functions.
  • rotamer -- a program in the CCP4 suite that identifies suspect rotamers.
  • AFITT -- model building software from OpenEye.

More Info

  •  top240.pdf (40KB) -- List of 240 pdb files used for compiling the library.
  •  med.reso.txt (8KB) -- List of 78 pdb files, at lower resolution, used for comparison purposes.
  • A page offering the rotamers kinemages and pdb files for download, and you can also call up views of the rotamers in JavaMage.
  • Kinemages of the distributions of side-chain dihedrals.

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:  download arrow bbdep_table.pdf (40KB)

Other rotamer libraries available on the web