2006
DOI: 10.1186/1471-2105-7-362
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A fast SCOP fold classification system using content-based E-Predict algorithm

Abstract: Background: Domain experts manually construct the Structural Classification of Protein (SCOP) database to categorize and compare protein structures. Even though using the SCOP database is believed to be more reliable than classification results from other methods, it is labor intensive. To mimic human classification processes, we develop an automatic SCOP fold classification system to assign possible known SCOP folds and recognize novel folds for newly-discovered proteins.

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Cited by 15 publications
(7 citation statements)
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References 33 publications
(43 reference statements)
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“…It is notable that though we have reduced the dimension of quantitative feature-vector representation of protein tertiary structures to at the most seven, the accuracy of structural classification we get is comparable to or better than that of Chi et al [12,13]. In the case of common fold types representing a structural class, the dimension as less than five is adequate for predictive classification with high accuracy.…”
Section: Discussionsupporting
confidence: 59%
See 3 more Smart Citations
“…It is notable that though we have reduced the dimension of quantitative feature-vector representation of protein tertiary structures to at the most seven, the accuracy of structural classification we get is comparable to or better than that of Chi et al [12,13]. In the case of common fold types representing a structural class, the dimension as less than five is adequate for predictive classification with high accuracy.…”
Section: Discussionsupporting
confidence: 59%
“…Considering that SCOP database does finer structural classifications at different fold levels and is also the basis/ yardstick of test of the work reported by Chi et al [13], we have considered structural families and fold types of protein (domains) as identified in this database. For exhaustive search we randomly selected maximum possible number of high-resolution structures of proteins the structural domains of which are authenticated in SCOP such that a comparable number of non-redundant observations are available from each of the four classes of interest and such that samples from each class will contain different possible sizes and orientation of the structural domain it represents.…”
Section: Data Set For Common Structural Fold Within a Classmentioning
confidence: 99%
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“…Consequently, many of the proteins solved have little or no previous experimental characterization and have been classified as domains of unknown function (DUFs; Bateman et al, 2010) or have only a tentative functional annotation based on amino-acid sequence homology. A variety of online tools and web-based search engines, such as EBI-SSM (Krissinel & Henrick, 2004), DALI (Holm et al, 2008), VAST (Gibrat et al, 1996) and fast-SCOP (Chi et al, 2006), allow the inference of function based on structural similarity. However, these approaches have their limitations.…”
Section: Introductionmentioning
confidence: 99%