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SASBDB, a repository for biological small-angle scattering data.

Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI - Nucleic Acids Res. (2014)

Bottom Line: Due to recent advances in instrumentation and computational methods, the quantity of experimental scattering data and subsequent publications is increasing dramatically.The need for a global repository allowing investigators to locate and access experimental scattering data and associated models was recently emphasized by the wwPDB small-angle scattering task force (SAStf).At present the quality of deposited experimental data and the accuracy of models are manually curated, with future plans to integrate automated systems as the database expands.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany.

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Brief representation of a SASBDB entry (browsing unit). (A) SASBDB ID and the title of the entry. (B) Experimental scattering data (logarithmic plot thumbnail). (C) One of the models. (D) Name of the macromolecule(s) that were measured, expected molecular weight organism, polymer type. Buffer details. Experiment type, instrument and data collection date. (E) Structural parameters: radius of gyration, maximum particle dimension, Porod volume. (F) Title of the publication (or project in case of unpublished data), journal reference, authors.
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Figure 3: Brief representation of a SASBDB entry (browsing unit). (A) SASBDB ID and the title of the entry. (B) Experimental scattering data (logarithmic plot thumbnail). (C) One of the models. (D) Name of the macromolecule(s) that were measured, expected molecular weight organism, polymer type. Buffer details. Experiment type, instrument and data collection date. (E) Structural parameters: radius of gyration, maximum particle dimension, Porod volume. (F) Title of the publication (or project in case of unpublished data), journal reference, authors.

Mentions: The browse page lists all entries sorted by deposition date (more recent first) and it comprises browsing units (Figure 3). Each unit shows the scattering profile and one of the derived models. If a model has not been deposited along with the data, the space otherwise occupied by the model displays an automatically calculated dimensionless Kratky plot. This plot has been chosen because it may not be possible to obtain a single representative model for display purposes, for example, from disordered or flexible systems, or a project aim might not encompass the generation of 3D-models. Therefore, the Kratky plot substitution acts as a visual tool for users to qualitatively assess globularity, extensibility, flexibility or disorder of a macromolecule even if a model has not been provided. Information about sample, buffer, experiment and any associated publication is also presented in the browsing unit together with three structural parameters: Rg, Dmax and VPorod which give a general estimation of the particle size and shape. Clicking on the unique SASBDB identifier, the displayed SAS dataset or model/Kratky plot directs the user to the associated entry.


SASBDB, a repository for biological small-angle scattering data.

Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI - Nucleic Acids Res. (2014)

Brief representation of a SASBDB entry (browsing unit). (A) SASBDB ID and the title of the entry. (B) Experimental scattering data (logarithmic plot thumbnail). (C) One of the models. (D) Name of the macromolecule(s) that were measured, expected molecular weight organism, polymer type. Buffer details. Experiment type, instrument and data collection date. (E) Structural parameters: radius of gyration, maximum particle dimension, Porod volume. (F) Title of the publication (or project in case of unpublished data), journal reference, authors.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383894&req=5

Figure 3: Brief representation of a SASBDB entry (browsing unit). (A) SASBDB ID and the title of the entry. (B) Experimental scattering data (logarithmic plot thumbnail). (C) One of the models. (D) Name of the macromolecule(s) that were measured, expected molecular weight organism, polymer type. Buffer details. Experiment type, instrument and data collection date. (E) Structural parameters: radius of gyration, maximum particle dimension, Porod volume. (F) Title of the publication (or project in case of unpublished data), journal reference, authors.
Mentions: The browse page lists all entries sorted by deposition date (more recent first) and it comprises browsing units (Figure 3). Each unit shows the scattering profile and one of the derived models. If a model has not been deposited along with the data, the space otherwise occupied by the model displays an automatically calculated dimensionless Kratky plot. This plot has been chosen because it may not be possible to obtain a single representative model for display purposes, for example, from disordered or flexible systems, or a project aim might not encompass the generation of 3D-models. Therefore, the Kratky plot substitution acts as a visual tool for users to qualitatively assess globularity, extensibility, flexibility or disorder of a macromolecule even if a model has not been provided. Information about sample, buffer, experiment and any associated publication is also presented in the browsing unit together with three structural parameters: Rg, Dmax and VPorod which give a general estimation of the particle size and shape. Clicking on the unique SASBDB identifier, the displayed SAS dataset or model/Kratky plot directs the user to the associated entry.

Bottom Line: Due to recent advances in instrumentation and computational methods, the quantity of experimental scattering data and subsequent publications is increasing dramatically.The need for a global repository allowing investigators to locate and access experimental scattering data and associated models was recently emphasized by the wwPDB small-angle scattering task force (SAStf).At present the quality of deposited experimental data and the accuracy of models are manually curated, with future plans to integrate automated systems as the database expands.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Hamburg Outstation, Notkestr. 85, Geb. 25a, 22603 Hamburg, Germany.

Show MeSH
Related in: MedlinePlus