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http://bura.brunel.ac.uk/handle/2438/3011
Title: | Multiple structural alignment for distantly related all b structures using TOPS pattern discovery and simulated annealing |
Authors: | Williams, A Gilbert, D Westhead, DR |
Keywords: | Pattern discovery;Protein topology;Simulated annealing;Structural alignment;Superfolds |
Issue Date: | 2003 |
Publisher: | Oxford University Press |
Citation: | Protein Engineering. 16(12): 913-923 |
Abstract: | Topsalign is a method that will structurally align diverse protein structures, for example, structural alignment of protein superfolds. All proteins within a superfold share the same fold but often have very low sequence identity and different biological and biochemical functions. There is often signi®cant structural diversity around the common scaffold of secondary structure elements of the fold. Topsalign uses topological descriptions of proteins. A pattern discovery algorithm identi®es equivalent secondary structure elements between a set of proteins and these are used to produce an initial multiple structure alignment. Simulated annealing is used to optimize the alignment. The output of Topsalign is a multiple structure-based sequence alignment and a 3D superposition of the structures. This method has been tested on three superfolds: the b jelly roll, TIM (a/b) barrel and the OB fold. Topsalign outperforms established methods on very diverse structures. Despite the pattern discovery working only on b strand secondary structure elements, Topsalign is shown to align TIM (a/b) barrel superfamilies, which contain both a helices and b strands. |
URI: | http://bura.brunel.ac.uk/handle/2438/3011 |
DOI: | http://dx.doi.org/10.1093/protein/gzg116 |
Appears in Collections: | Computer Science Dept of Computer Science Research Papers |
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