Alternative Alignments from Comparison of Protein Structures

Edward S.C. Shih and Ming-Jing Hwang

PROTEINS:Structure,Function, and Bioinformatics, Vol. 56, pp 519-527,2004

Created by: Chia-Chang WangDate: Sept. 30,2004

Abstract

Abstract(cont.)

Method

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Methods

The angle-distance map of SSE pairs –

a 2D reduction of the 3D structure

Methods(cont.)

The SSE matching probabilites

d0 :the threshold value of the midpoint distance

θ0 :torsion angle

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Methods(cont.)

To derive individual SSE matching probabilities,the probability weights for SSEs pairs calculated were combined.

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Methods(cont.)

A greedy procedure for selecting viable alignment solutions The new match did not contain an SSE that

had already been selected The new match must fit the constraints of a

sequential relationship with matches already selected

All the recombined inter-SSE pairs generated by the new match must have a non-zero probability weight

Methods(cont.)

a b c d e f g

a’ b’ c’ d’ e’ f’ g’

Methods(cont.)

From rough alignment to refined alignment

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S : similarity measure

N :number of aligned SSE pairs

k :fitness measure to account for length difference in matched SSEs

Results

Results(cont.)

Results(cont.)

r:overlap ratio r’:equivalent ratio

Results(cont.)

Results(cont.)

END