Threading

From DrugPedia: A Wikipedia for Drug discovery

This method is based on the observation that very limited number of ‘unique protein folds’ are present in PDB. In threading the structure of a new sequence is determined by finding the best fit to some fold in a library of protein structure. The concept of threading protein sequences through different structure motifs involves the construction of misfolded model structures, where an incorrect sequence is deliberately built on to the backbone of another protein. Threading a sequence through a fold requires a specific alignment between the amino acid sequence of the protein under consideration and the corresponding amino acid residue positions of the folding motif. The known structure establishes a set of possible amino acid positions in 3D space. The query sequence is made similar to the known structure by placing its amino acids into their aligned positions. The primary aim of these methods is to select the most probable fold for a given sequence or to recognize suitable sequences that might fold into a given structure. The threading method is generally applied only on proteins whose amino acid sequences accept one of the protein folds previously studied by experimental techniques.