The effects of crystal packing on protein loop structures are examined by (1) a com-parison of loops in proteins that have been crystal-lized in alternate packing arrangements, and (2) theoretical prediction of loops both with and with-out the inclusion of the crystal environment. Re-sults show that in a minority of cases, loop geom-etries are dependent on crystal packing effects. Explicit representation of the crystal environment in a loop prediction algorithm can be used to model these effects and to reconstruct the structures, and relative energies, of a loop in alternative packing environments. By comparing prediction results with and without the inclusion of the crystal environ-ment, the loop prediction algorithm can further be used to identify cases in which a crystal structure does not represent the most stable state of a loop in solution. We anticipate that this capability has implications for structural biology. Proteins 2005; 60:103–109.
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