Protein Fold Recognition and Threading

Abstract

Fold recognition and threading methods can be used to assign tertiary structures to protein sequences, even in the absence of clear homology. The ongoing development of such methods has had a significant impact on structural biology, providing us with an increasing ability to accurately model 3D protein structures using very evolutionary distant fold templates. Although fold recognition and threading techniques will not yield equivalent results as those from X-ray crystallography, they are a comparatively fast and inexpensive way to a build a close approximation of a structure from a sequence, without the time and costs of experimental procedures. Using fold recognition we are able to identify proteins with known structures that share common folds with the target sequences. The identified structures can then be used as templates from which the folds of the target sequences are modeled. For the vast majority of new protein sequences, there will be a structure with a similar fold within the Protein Data Bank (PDB) (see Table 2.1 for a list of relevant Internet resources) from which a suitable model could be constructed. Indeed, in the mid-1990s it was