The secondary structure prediction methods can be either ab initio based, which make use of single sequence information only, or homology based, which makes use of multiple sequence alignment information.

Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the secondary structures of proteins and nucleic acid sequences based only on knowledge of their primary structure.

Topic include: Protein Secondary Structure Prediction for Globular Proteins, Secondary Structure Prediction for Transmembrane Proteins, & Coiled Coil Prediction.