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BMCBI
2008

Towards an automatic classification of protein structural domains based on structural similarity

13 years 11 months ago
Towards an automatic classification of protein structural domains based on structural similarity
Background: Formal classification of a large collection of protein structures aids the understanding of evolutionary relationships among them. Classifications involving manual steps, such as SCOP and CATH, face the challenge of increasing volume of available structures. Automatic methods such as FSSP or Dali Domain Dictionary, yield divergent classifications, for reasons not yet fully investigated. One possible reason is that the pairwise similarity scores used in automatic classification do not adequately reflect the judgments made in manual classification. Another possibility is the difference between manual and automatic classification procedures. We explore the degree to which these two factors might affect the final classification. Results: We use DALI, SHEBA and VAST pairwise scores on the SCOP C class domains, to investigate a variety of hierarchical clustering procedures. The constructed dendrogram is cut in a variety of ways to produce a partition, which is compared to the SC...
Vichetra Sam, Chin-Hsien Tai, Jean Garnier, Jean-F
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Vichetra Sam, Chin-Hsien Tai, Jean Garnier, Jean-François Gibrat, Byungkook Lee, Peter J. Munson
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