IRECS is a program that predicts the conformation of protein side chains . It does so either using only backbone information or using additional template information about the side-chain conformations.
The input is a standard PDB format protein as the template structure. The sequence to be modelled can be either given as single mutation strings, a target sequence file or an alignment file. If no information about mutations is given, the side chain conformations of the template structure are re-predicted. If a target sequence is provided, the residues of the template structure will be mutated according to this sequence. The prediction is guided by a combination of our atom-interaction potential ROTA and rotamer scores calculated with probabilities from the Backbone-Dependent Rotamer Library of the Dunbrack research group . Side-chain conformations are build using standard CHARMM  bond lengths and angles. IRECS can ouput multiple ambigous positions of side chains and assigns a occupancy value to these conformations based on the observed interactions with the rest of the protein.
Please cite IRECS as follows
 Hartmann, C., Antes, I., Lengauer, T. IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models. Protein Sci. 2007 16: 1294-1307.
Some required data files were kindly provided by these people
 Dunbrack, R.L., Jr., Cohen, F.E. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6:1661-1681, 1997.
 MacKerell, J.A.D., Bashford, D., Bellott, M., Dunbrack Jr, R.L.a.E.J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S.a.J.-M.D., Kuchnir, L., et al. 1998. All-atom empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem. B 102: 3586-3616.