Richardson Lab: Rotamer Libraries

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Rotamer Libraries

Phe rotamers Rotamers are usually defined as low energy side-chain conformations. The use of a 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 library differs from those previously published in a number of ways.

We use only very high resolution structures (1.7 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.

Full details are available in:
SC Lovell, JM Word, JS Richardson and DC Richardson (2000) " The Penultimate Rotamer Library" Proteins: Structure Function and Genetics 40 389-408.
Please cite this paper if you use the library.

The resulting library is available in various layouts and file formats.

The library as it appears in the publication.	[TEXT]	\|\|	[PDF]

A fuller description, with assymetric widths and explicit bins.	[TEXT]	\|\|	[PDF]

A version for use in automated procedures, with common-atom angles and samples.	[TEXT]	\|\|	[PDF]

Rotamer databases are available for two popular model rebuilding programs
Databases for versions 6 to 8 of O.	[info]	\|\|	[TAR]

For XtalView, dictionary files, with and without hydrogens, are available.	[info]	\|\|	[TAR]
(The tar button will download a Z-zipped tar file, containing the databases and use intstructions. The doc button will display the use instructions.)

If you have problems downloading any of these files, check the ftp troubleshooting page. These files are also available from our FTP site (ftp://kinemage.biochem.duke.edu/pub) via internet browser or by ftp client as an anonymous user. The rotamer files are in the datasets subdirectory.

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.
These tables are for Asp and Asn: [TEXT] || [PDF]

Rotamer Library Background and Extras

List of 240 pdb files used for compiling the library.
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.

Earlier Asn and Gln libraries

Asparagine Rotamer Library:	[TEXT]	\|\|	[PDF]
Glutamine Rotamer Library:	[TEXT]	\|\|	[PDF]

Other rotamer libraries available on the web

Ponder and Richards's original library is available from Roland Dunbrack's site.
Dunbrack and Cohen's libraries (backbone dependent and independent) are also available from there.
Tuffery et al's library from INSERM in France.
DeMaeyer et al's library is also available on Dunbrack's site.

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