DALI algorithm

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. 

Topology, and Homologous (CATH) superfamilies classification and the domain classification based on the Distance ALIgnment (DALI) algorithm. Finally, the tutorial concludes with a discussion of the future of protein structure classifications. 

In the PSSC procedure itself, initially the full structure of a protein of interest was subjected to search for structural similarity using the Dali (FSSP) and Combinatorial Extension (CE) algorithms. The searches were performed across the entire PDB and yielded lists of structurally similar proteins ordered by decreasing similarity (Figure 9.14). The entries which were deemed interesting... 

DALY s (1993) The invisible difference predictor an algorithm for the assessment of image fidelity, in Digital Images and Human Vision, ed. AD Watson, MIT Press. 

Daly, S. 1992. The visible differences predictor An algorithm for the assessment of image fidelity. In Human Vision, Visual Processing, and Digital Display III, ed. B.E. Rogowitz, pp. 2-15. Proc. SPIE 1666. 

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