Rotamer Library

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Side chains do not have free mobility; they prefer distinct conformations (called rotamers) according to organic chemistry first principles [1,2]. Rotamer libraries are a concise description of side-chain conformational preferences. For each rotamer, the library annotates its frequency and preferred position of each side chain χ angle; They are typically derived from a large sample of crystal structures using filters to remove poor quality data and statistical techniques to improve the data in low frequency regions [3,4].

We have created a backbone-independent rotamer library from 298K simulations of the initial release of 188 proteins in the Dynameomics database. Structures from molecular dynamics have two advantages over experimental data. First, structures have perfect information. There is no ambiguity about coordinates from weak electron density, particularly for large residues on the surface of the protein. Second, the structures are taken in solution, avoiding possible biases from the crystalline environment.

For each amino acid on the left, we have included our rotamer library, our rotamer definitions, and the dihedral angle definitions seen in Dynameomics, our GGXGG peptide simulations, Astral 40 [5], and the Dunbrack Rotamer Library [3]. For a full description of our Dynamic Rotamer Library, see Scouras and Daggett [6].

References

1. Dunbrack, R. L. Rotamer libraries in the 21^st century. Current Opinion in Structural Biology 12: 431-40, 2002. [DOI]
2. Ramachandran, G. N., Ramakrishnan, C. & Sasisekharan, V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7: 95-9, 1963. [DOI]
3. Dunbrack, R. L., & Cohen, F. E. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Science 7: 1661-81, 1997. [DOI] [Web]
4. Lovell, S. C., Word, J. M., Richardson, J. S. & Richardson, D. C. The penultimate rotamer library. Proteins 40: 389-408, 2000. [DOI] [Web]
5. Chandonia, J. M., Hon, G., Walker, N. S., Lo Conte, L., Koehl, P., Levitt, M. & Brenner, S. E. The ASTRAL compendium in 2004. Nucleic Acids Research 32: D189-92, 2004. [DOI] [Web]