Optimal Aligmnent Methods

Finally, a refinement is done using Monte Carlo methods at each residue position in an attempt to optimize the structural aligmnent. 

The second approach compares structures with structures, in the same light as the vector aligmnent search tool (VAST) discussed in Chapter 5 does. The DALI algorithm looks for similar contact patterns between two proteins, performs an optimization, and returns the best set of structure alignment solutions for those proteins (Holm and Sander, 1993). The method is flexible in that gaps may be of any length. 

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