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A protein is a sequence over the alphabet of the 20 common amino acids. This is the so-called primary sequence of the protein. For some proteins the primary sequence determines the folded three dimensional structure of the protein -- its tertiary structure. In principle it should be possible to predict the tertiary structure from the primary sequence, but we do not know how to do this in general.

As an intermediate step, the secondary structure of a protein is sometimes considered. This is the collection of relatively "local" parts of the the 3-D structure of the protein. Typically these may be classified as {extended, helix, other}, although finer classifications are also used. If secondary structure could be reliably predicted, predicting tertiary structure would be reduced from packing hundreds or thousands of amino acids to packing at most dozens of secondary structures, if . . . !

The picture is further complicated by the fact that some proteins require other proteins, chaperonins, to assist them to fold, and may be in a local, rather than a global energy minimum, when finally folded. And a protein cannot truly be considered in isolation or at rest -- its vibrational energy and the energy due to interactions with other molecules, notably water, may be of the same order of magnitude as the energy due to the protein's fold itself.

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