IRECS ( REduction of Conformational Space) can predict multiple conformations for all side chains of a target protein. Side-chain conformations are selected according to the flexibility of the respective side chain. IRECS is also able to mutate single side chains or read in alignments to create a homology model of the target protein on a template backbone.
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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.