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psipred
PSIPRED (Psi-blast based secondary structure prediction) is a technique used to investigate protein structure. PSIPRED employs neural network, machine learning methods in its algorithm. It is a server-side program, featuring a website serving as a front-end interface, which can predict a protein's secondary structure (beta sheets, alpha helices and coils) from the primary sequence.
== Secondary structure ==
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 an automatic determination of secondary structure difficult. Efforts to use computers in predicting the secondary structures of proteins based only on their given primary structure sequences have been ongoing since the 1970s.
Secondary structure prediction involves a set of techniques 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 helices, 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 for the detection of specific well-defined patterns such as trans-membrane helices and coiled coils in proteins, or canonical micro-RNA structures in RNA.
抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』
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