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WDSPdb: a database for WD40-repeat proteins.

Wang Y, Hu XJ, Zou XD, Wu XH, Ye ZQ, Wu YD - Nucleic Acids Res. (2014)

Bottom Line: WD40-repeat proteins, as one of the largest protein families, often serve as platforms to assemble functional complexes through the hotspot residues on their domain surfaces, and thus play vital roles in many biological processes.Consequently, it is highly required for researchers who study WD40 proteins and protein-protein interactions to obtain structural information of WD40 domains.Systematic identification of WD40-repeat proteins, including prediction of their secondary structures, tertiary structures and potential hotspot residues responsible for protein-protein interactions, may constitute a valuable resource upon this request.

View Article: PubMed Central - PubMed

Affiliation: Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China.

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Related in: MedlinePlus

The framework of WDSPdb.
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Figure 1: The framework of WDSPdb.

Mentions: Figure 1 shows the details of identifying and classifying the WD40-repeat proteins in WDSPdb. First, for each protein sequence in the UniProt database, the WDSP program was used to identify WD40 repeats. If no less than six WD40 repeats were identified, the protein was classified as a WD40 protein that contains one or more WD40 domains (if more than eight repeats). Second, for each WD40 domain, the secondary structure of the domain and potential hotspot residues for PPIs were predicted and displayed in a table of the result page (Figure 2A). Third, the predicted 3D structure models were presented in the interactive JSmol applet (http://jsmol.sourceforge.net/). Finally, general annotations extracted from the UniProt database were also shown in the result page.


WDSPdb: a database for WD40-repeat proteins.

Wang Y, Hu XJ, Zou XD, Wu XH, Ye ZQ, Wu YD - Nucleic Acids Res. (2014)

The framework of WDSPdb.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383882&req=5

Figure 1: The framework of WDSPdb.
Mentions: Figure 1 shows the details of identifying and classifying the WD40-repeat proteins in WDSPdb. First, for each protein sequence in the UniProt database, the WDSP program was used to identify WD40 repeats. If no less than six WD40 repeats were identified, the protein was classified as a WD40 protein that contains one or more WD40 domains (if more than eight repeats). Second, for each WD40 domain, the secondary structure of the domain and potential hotspot residues for PPIs were predicted and displayed in a table of the result page (Figure 2A). Third, the predicted 3D structure models were presented in the interactive JSmol applet (http://jsmol.sourceforge.net/). Finally, general annotations extracted from the UniProt database were also shown in the result page.

Bottom Line: WD40-repeat proteins, as one of the largest protein families, often serve as platforms to assemble functional complexes through the hotspot residues on their domain surfaces, and thus play vital roles in many biological processes.Consequently, it is highly required for researchers who study WD40 proteins and protein-protein interactions to obtain structural information of WD40 domains.Systematic identification of WD40-repeat proteins, including prediction of their secondary structures, tertiary structures and potential hotspot residues responsible for protein-protein interactions, may constitute a valuable resource upon this request.

View Article: PubMed Central - PubMed

Affiliation: Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China.

Show MeSH
Related in: MedlinePlus