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Protocols

SASBDB specifications

Information


Unique identifier OMICS_10449
Name SASBDB
Alternative name Small-Angle Scattering Biological Data Bank
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Dmitri I. Svergun

Publication for Small-Angle Scattering Biological Data Bank

SASBDB citations

 (24)
library_books

Structural model of human dUTPase in complex with a novel proteinaceous inhibitor

2018
Sci Rep
PMCID: 5847570
PMID: 29531348
DOI: 10.1038/s41598-018-22145-8

[…] eling based on SAXS data, multiple runs were performed to verify the stability of the solution, and to establish the most typical 3D reconstructions using DAMAVER. SAXS data has been deposited at the SASBDB (www.sasbdb.org) with accession codes: SASDC57, SASDC67, SASDC77, SASDC87. […]

library_books

Disease Variants of FGFR3 Reveal Molecular Basis for the Recognition and Additional Roles for Cdc37 in Hsp90 Chaperone System

2018
PMCID: 5846801
PMID: 29478821
DOI: 10.1016/j.str.2018.01.016

[…] The CORAL calculations were repeated twenty times using different random seeds and the resulting models grouped into clusters using DAMCLUST ().The experimental SAXS curves have been submitted to the Small Angle Scattering Biological Data Bank (SASBDB) with the accession codes; SASDBP9 for human Hsp90 co-chaperone Cdc37 protein (Cdc37), SASDBQ9 for human Hsp90 co-chaperone Cdc37 in complex with fi […]

library_books

Structure of the C1r–C1s interaction of the C1 complex of complement activation

2018
Proc Natl Acad Sci U S A
PMCID: 5789954
PMID: 29311313
DOI: 10.1073/pnas.1718709115

[…] creating the characteristic bouquet-like architecture observed by electron microscopy. With this structure as a template, we performed rigid-body modeling using previously obtained SAXS data for C1 (Small Angle Scattering Biological Data Bank ID: SASDB38) () using Coral, part of the ATSAS package (). Flexibility was permitted at the C1q kink and at the junction between the collagen-like domains a […]

call_split

Convergent evolution of plant and animal embryo defences by hyperstable non digestible storage proteins

2017
Sci Rep
PMCID: 5696525
PMID: 29158565
DOI: 10.1038/s41598-017-16185-9
call_split See protocol

[…] . The resulting dummy atom model represents the shape of the scattering particle. The average of the best ten models fitting the experimental data was obtained with DAMMIF. Data were deposited in the Small Angle Scattering Biological Data Bank SASBDB. […]

library_books

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

2017
Nucleic Acids Res
PMCID: 5753225
PMID: 29126160
DOI: 10.1093/nar/gkx1070

[…] information and experimental setup described for each of the employed methods in a dedicated tab. In particular, for structures where associated small-angle scattering (SAS) data is available at the Small-Angle Scattering Biological Data Bank (SASBDB, sasbdb.org, ()), information is retrieved directly from SASBDB via its API. The PDBe page for such entries shows key parameters derived from the sc […]

library_books

New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

2017
PMCID: 5734392
PMID: 28815765
DOI: 10.1002/pro.3273

[…] he database of the electrostatic molecular surfaces, eF‐site, for educational purposes. Fifth, we introduce the extension of molecular shape comparison server, Omokage search, where searching for the Small Angle Scattering Biological Data Bank (SASBDB) entries is now available in addition to PDB and Electron Microscope Data Bank (EMDB). Finally, we integrate the database of NMR experimental data, […]

Citations

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SASBDB institution(s)
European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Hamburg, Germany
SASBDB funding source(s)
European Commission Seventh Framework Programme (FP7) projects BioStruct-X [283570]; IDPbyNMR [264257]; Bundesministerium für Bildung und Forschung (BMBF) project BIOSCAT [05K12YE1]

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