Fold Recognition

Overview:

Fold recognition (FR) is the name give to the process of assigning a known structure (a template) to a sequence of unknown structure (the query). The methodologies used include

• Straight sequence methods (like BLAST and PSI-BLAST)
• Sequence methods incorporating structure, including:- predicted and known secondary structure- structural environments- structural alignments
• "True" threading approaches
  The difference between "sequence" based methods and methods using threading is not always clear. In principle the sequence based method defines the "fitness" of the query onto the template from on the primary structure of the query and template sequences, respectively. Threading methods on the other hand defines the "fitness" of the query from the structural environment of the template structure. However as you saw from the list above some sequence based methods also incorporates structural information of the template in the alignment so the borderline is not very clear. The most powerful method are neither "true" sequence based nor "true" threading method, but some mixture of the two.

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Strategy for the Drug Discovery

Comparative protein modelling

Comparative protein modelling uses previously solved structures as starting points, or templates. This is effective because it appears that although the number of actual proteins is vast, there is a limited set of tertiary structural motifs to which most proteins belong. It has been suggested that there are only around 2000 distinct protein folds in nature, though there are many millions of different proteins.

These methods may also be split into two groups:

Homology modelling is based on the reasonable assumption that two homologous proteins will share very similar structures. Given the amino acid sequence of an unknown structure and the solved structure of a homologous protein, each amino acid in the solved structure is mutated, computationally, into the corresponding amino acid from the unknown structure.

Protein threading scans the amino acid sequence of an unknown structure against a database of solved structures. In each case, a scoring function is used to assess the compatibility of the sequence to the structure, thus yielding possible three-dimensional models.

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