The secondary structure of a protein
is an interesting phenomenon. When a protein folds
, it is believed that stretches of the primary sequence
pre-assemble into structures such as alpha helices
or beta strands
. This is the first and fastest process of protein folding. These secondary structural elements then join together in various patterns forming the tertiary fold
. Alpha helices
look like winding staircases of amino acids, while beta sheets
look like flat surfaces (generally). Whether a region of a protein forms a helix or a sheet is determined by many different factors, which are still under investigation today.
To a large extent, the primary sequence is a contributing factor because specific amino acids have propensities to form helices over sheets, or vice versa. Given these known propensities, people have tried to predict secondary structure as a preliminary solution to the protein folding problem. Sophisticated rule based algorithms have been implemented in neural nets which are becoming better and better at achieving success.