By analyzing the sequence of amino acids that make up a protein, it is, to some degree, possible to predict the the final shape into which it will fold (secondary, tertiary, and possibly even quaternary structure). This prediction is generally performed by determining how much each amino acid side chain likes or dislikes the surrounding environment (which is usually water, so amino-acids can be devided based on whether they are hydrophobic or hydrophilic). Further structure can be revealed by analyzing side chain details (for example there is one amino acid that has only a hydrogen for it's side chain, and this allows for much tighter turns because there are less steric interactions).

One of the most common and basic methods used in prediction is analysis of hydropathy plots which are particularly good at revealing alpha-helix structures, but particularly poor at revealing beta-barrel and other structures.

Prediction of a proteins shape, in general, allows for prediction of its function. The most obvious example is the prediction of membrane proteins of eukaryotes, which span the membrane, becuase they must have one or more distinct hydrophobic areas (for areas inside the membrane) and distinct hydrophilic areas (for the areas exposed to water on either side of the membrane).

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