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“ Rapid Methods for Comparing Protein Structures and Scanning Structure Databases” [Oliviero Carugo, Current Bioinformatics;1(1), 2006] Azhar Ali Shah Computational Foundations of Nanoscience Journal Club (CFNJC) CFNJC, October 19, 2007
Complexity of the structural biological information is increasing more rapidly as compared to computer performance
Consider:
Number of PDB entries as structural biological information ( PDB Graph )
Number of transistors per IC as a parameter of compute performance ( Moore’s Law )
Evaluation for 3 decades (1971 to 2003) gives:
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Introduction: problem 2/2 Number of PDB Structures Number of transistors per IC (x 100, 000) Confusing description! Total structures in 2003: 20, 000 Yearly growth in 2003: 5000
Uses Needleman and Wunsch algorithm on string representation of two 3D structures and calculates the percentage similarity score using following scheme
Uses distances b/w C atoms to represent the 3D structure
28 histograms are computed for each structure e.g.
Fold similarity of two structures is estimated as the average of probability of identity scores obtained from the pairwise comparison of 28 histograms Two histograms are compared through contingency table and χ 2 Test to obtain the probability of identity score
Secondary structure assignments are quite ambiguous and inconsistent! ( consensus based on majority vote needed ) Serious limitation of the methods that compare 3D structures based on SSE arrangements
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