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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
Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Introduction: about the author 1/2 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Introduction: about the author 2/2 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Introduction: problem 1/2 ,[object Object],[object Object],[object Object],[object Object],[object Object]
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
Introduction: requirement ,[object Object]
Introduction: motivations ,[object Object],[object Object],[object Object],[object Object],[object Object]
Introduction: background 1/3 ,[object Object],[object Object],[object Object]
Introduction: background 2/3 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Introduction: background 3/3 ,[object Object],[object Object],[object Object],[object Object]
Introduction: focus of the paper ,[object Object],[object Object]
Classification of methods ,[object Object],[object Object],[object Object],[object Object],[object Object]
String representation 1/4 ,[object Object],[object Object],[object Object],[object Object],[object Object]
String representation 2/4 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
String representation 3/4
String representation 4/4 ,[object Object],Should be 10? How fast TOPSCAN is?
Array representation 1/4 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Array representation 2/4 ,[object Object],[object Object],[object Object],[object Object],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
 
Array representations 4/4 ,[object Object],[object Object],[object Object],[object Object]
Secondary structural elements (SSEs) 1/6 ,[object Object],[object Object],[object Object]
Secondary structural elements (SSEs) 2/6 ,[object Object],[object Object],[object Object]
Secondary structural elements (SSEs) 3/6 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Secondary structural elements (SSEs) 4/6 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],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
Secondary structural elements (SSEs) 5/6 ,[object Object],[object Object],[object Object],[object Object],[object Object]
Secondary structural elements (SSEs) 6/6 ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Statistical performance of SSM or other methods? Two-step methods are slow?
Backbone representations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Hardly used in general case for similarity evaluation and hence no public web servers are available. However?
Comparison b/w various methods ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Strange! Speed also depends on the power of computing environment the algorithm runs on.
Summary ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Observations: ,[object Object],[object Object],[object Object]
Source: www.intel.com/research/silicon/mooreslaw.htm
Source: www.ncsb.org Total Yearly

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Presentation 2007 Journal Club Azhar Ali Shah