Tertiary protein structure methodology

One of the common ways of predicting protein tertiary structure assumes that the secondary structure has to be known before the prediction of a three-dimensional fold can be attempted [154-157]. While this view as a paradigm for protein structure prediction could be challenged, it certainly provides a straightforward framework that may sometimes prove to be useful. Indeed, there were a number of early attempts to apply such a methodology to low resolution protein fold predictions that were quite successful in some specific cases [154-157]. However, only recently has the problem of protein structure assembly, given its secondary structure, been more systematically addressed. 

Three general methodologies for photoregulating such activities of biomaterials as catalytic, binding, or recognition functions have been suggested (Scheme 2). One method involves the tethering of photoisomerizable units to a protein (Scheme 2(A)). In one photoisomer state, state A, the tertiary structure of the protein is... 

When structural alignments do not reveal structural similarities that allow annotation transfer, other approaches can be used to obtain information about the function of the target protein. The analysis of the conservation of 3D patterns of functionally relevant residues and evolutionary trace analysis (described in section 2.3.3) are examples of these methodologies. Structural patterns consist of coordinate files in PDB format containing the spatial positions of functionally important residues without considering their positions on the primary or secondary structure. In fact, these patterns can correspond to functional sites present in proteins with completely different folds. The program PINTS (Patterns In Non-homologous Tertiary Structures)... 

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