Secondary structure is the general three-dimensional form of local segments of
biopolymers such as
proteins and
nucleic acids (
DNA,
RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be the
tertiary structure. Secondary structure can be formally defined by the
hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In proteins, the secondary structure is defined by the patterns of hydrogen bond between
backbone amino and
carboxyl groups. Conversely, for nucleic acids, the secondary structure consists of the hydrogen bonding between the
nitrogenous bases. The hydrogen bonding patterns may be significantly distorted, which makes automatic determination of secondary structure difficult. Efforts to use computers to predict
protein secondary structures, based only on their given
primary structure sequences, have been ongoing since the 1970s. Secondary structure prediction involves a set of methods in
bioinformatics that aim to predict the
local secondary structures of proteins and RNA sequences based only on knowledge of their
primary structure –
amino acid or
nucleotide sequence, respectively. For proteins, a prediction consists of assigning regions of the amino acid sequence as highly probable
alpha helixes,
beta strands (often noted as
extended conformations), or turns. The success of a prediction is determined by comparing it to the results of the
DSSP algorithm applied to the crystal structure of the protein; for nucleic acids, it may be determined from the hydrogen bonding pattern. Specialized algorithms have been developed to detect specific well-defined patterns such as
transmembrane helixes and
coiled coils in proteins, or canonical micro-RNA structures in RNA. == Basic information ==