SCOP database in 2004: refinements integrate structure and sequence family data

Andreeva, Antonina

doi:10.1093/nar/gkh039

Cited by 850 publications

(632 citation statements)

References 21 publications

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“…These folds describe the spatial arrangement of secondary structure elements such as a-helices and b-sheets into defined motifs that have been found as conserved in nature and during evolution [52 -55]. Consequently, different fold types were summarized in a structural classification of proteins (SCOP) database in which about 1000 distinct folds have been described up to now [56,57]. Although computational genome analysis predicts that between 1000 and 10,000 different folds should exist in nature, the vast majority of proteins are expected to be built up from roughly 1000 of the most abundant folds [58 -60].…”

Section: Kaiser Et Almentioning

confidence: 99%

Biology-inspired synthesis of compound libraries

Kaiser

Wetzel

Kumar

et al. 2008

Cell. Mol. Life Sci.

148

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Section: Kaiser Et Almentioning

confidence: 99%

Biology-inspired synthesis of compound libraries

Kaiser

Wetzel

Kumar

et al. 2008

Cell. Mol. Life Sci.

148

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“…In all these proteins, the homologous region corresponds to several consecutive repeats belonging to various Pfam families (WD40, FG-GAP, BNR or PQQ repeats), which are included in the Pfam β-propeller clan [36]. A domain search with InterProScan [28] identified an N-terminal quinoprotein alcohol dehydrogenase-like domain (164 residues; E-value: 2.8 E-13), which adopts a 8-bladed β-propeller fold (SCOP classification, [37]). …”

Section: Sequence Analyses Of the Cgla Gene Productmentioning

confidence: 99%

Degradation of λ-carrageenan by Pseudoalteromonas carrageenovora λ-carrageenase: a new family of glycoside hydrolases unrelated to κ- and ι-carrageenases

Guibet¹,

Colin²,

Barbeyron³

et al. 2007

Biochem. J.

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Carrageenans are sulfated galactans found in the cell walls of red seaweeds. They are classified according to the number and the position of sulfate ester groups. lambda-Carrageenan is the most sulfated carrageenan and carries at least three sulfates per disaccharide unit. The sole known depolymerizing enzyme of lambda-carrageenan, the lambda-carrageenase from Pseudoalteromonas carrageenovora, has been purified, cloned and sequenced. Sequence analyses have revealed that the lambda-carrageenase, referred to as CglA, is the first member of a new family of GHs (glycoside hydrolases), which is unrelated to families GH16, that contains kappa-carrageenases, and GH82, that contains iota-carrageenases. This large enzyme (105 kDa) features a low-complexity region, suggesting the presence of a linker connecting at least two independent modules. The N-terminal region is predicted to fold as a beta-propeller. The main degradation products have been purified and characterized as neo-lambda-carratetraose [DP (degree of polymerization) 4] and neo-lambda-carrahexaose (DP6), indicating that CglA hydrolyses the beta-(1-->4) linkage of lambda-carrageenan. LC-MALLS (liquid chromatography-multi-angle laser light scattering) and (1)H-NMR monitoring of the enzymatic degradation of lambda-carrageenan indicate that CglA proceeds according to an endolytic mode of action and a mechanism of inversion of the anomeric configuration. Using 2-aminoacridone-labelled neo-lambda-carrabiose oligosaccharides, in the present study we demonstrate that the active site of CglA comprises at least 8 subsites (-4 to +4) and that a DP6 oligosaccharide binds in the subsites -4 to +2 and can be hydrolysed into DP4 and DP2.

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“…Protein classification could be an illustrative example to show the needs. A major goal of SCOP (structural classification of proteins) 8 and CATH (class, architecture, topology, homologous superfamily) 9 is to understand the structural, functional, and evolutionary relationships among proteins by classifying domains according to their structure. This structure-based approach may be effective in detecting distant relationships across proteins.…”

Section: Introductionmentioning

confidence: 99%

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

Lee

2016

Protein Science

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Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of GLoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/.

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SCOP database in 2004: refinements integrate structure and sequence family data

Cited by 850 publications

References 21 publications

Biology-inspired synthesis of compound libraries

Biology-inspired synthesis of compound libraries

Degradation of λ-carrageenan by Pseudoalteromonas carrageenovora λ-carrageenase: a new family of glycoside hydrolases unrelated to κ- and ι-carrageenases

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

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