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Structural Alignment Methods: Key Points from the Talk


2 Goals
a) Find remote similarities to a query structure
b) Best "fit" for two given structures A & B
Superimpose from a given <------> Find an alignment based on 3D alignment coordinates

General strategy of structure analysis similar to sequence analysis methods...and then some.

Computer similarity matrix--Use pairwise alignment


--compute pairwise distances between every atom in respective structures to get what is called inner-protein distance matrix.
--convert distance matrix into similarity matrix.
--note that one is creating a specific matrix for each pair of residues I and J; S(I,J) dependent entirely on 3D coordinates.
--apply dynamic programming to get sum matrix.



We now must perform an RMS fit for successful structural alignment, since possible matches for different segments are linked in these "rigid" 3D structures.


with sequence analysis, dynamic programming/sum matrix is sufficient optimization for global convergence, since optimum match for one part of sequence does not affect that of another region...