# Welcome to Ranjit's Bioinformatics Web Site

### 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...

### Solution? Iterate with RMS and dynamic programming until
convergence....

### More on RMS Calculations