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DC Field | Value | Language |
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dc.contributor.author | Williams, A | - |
dc.contributor.author | Gilbert, D | - |
dc.contributor.author | Westhead, DR | - |
dc.coverage.spatial | 11 | en |
dc.date.accessioned | 2009-02-05T15:50:10Z | - |
dc.date.available | 2009-02-05T15:50:10Z | - |
dc.date.issued | 2003 | - |
dc.identifier.citation | Protein Engineering. 16(12): 913-923 | en |
dc.identifier.uri | http://bura.brunel.ac.uk/handle/2438/3011 | - |
dc.description.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. | en |
dc.format.extent | 639055 bytes | - |
dc.format.mimetype | application/pdf | - |
dc.language.iso | en | - |
dc.publisher | Oxford University Press | en |
dc.subject | Pattern discovery | en |
dc.subject | Protein topology | - |
dc.subject | Simulated annealing | - |
dc.subject | Structural alignment | - |
dc.subject | Superfolds | - |
dc.title | Multiple structural alignment for distantly related all b structures using TOPS pattern discovery and simulated annealing | en |
dc.type | Research Paper | en |
dc.identifier.doi | http://dx.doi.org/10.1093/protein/gzg116 | - |
Appears in Collections: | Computer Science Dept of Computer Science Research Papers |
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