Protein Structure Prediction - Secondary Structure

Secondary Structure

Secondary structure prediction is 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 likely 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 transmembrane helices and coiled coils in proteins, or canonical microRNA structures in RNA.

The best modern methods of secondary structure prediction in proteins reach about 80% accuracy; this high accuracy allows the use of the predictions in fold recognition and ab initio protein structure prediction, classification of structural motifs, and refinement of sequence alignments. The accuracy of current protein secondary structure prediction methods is assessed in weekly benchmarks such as LiveBench and EVA.