Literature DB >> 25352555

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

Erica Valentini1, Alexey G Kikhney2, Gianpietro Previtali1, Cy M Jeffries1, Dmitri I Svergun3.   

Abstract

Small-angle X-ray and neutron scattering (SAXS and SANS) are fundamental tools used to study the global shapes of proteins, nucleic acids, macromolecular complexes and assemblies in solution. 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). The small-angle scattering biological data bank (SASBDB) www.sasbdb.org has been designed in accordance with the plans of the SAStf as part of a future federated system of databases for biological SAXS and SANS. SASBDB is a comprehensive repository of freely accessible and fully searchable SAS experimental data and models that are deposited together with the relevant experimental conditions, sample details and instrument characteristics. 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.
© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2014        PMID: 25352555      PMCID: PMC4383894          DOI: 10.1093/nar/gku1047

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  23 in total

1.  A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome.

Authors:  D I Svergun; K H Nierhaus
Journal:  J Biol Chem       Date:  2000-05-12       Impact factor: 5.157

2.  Determination of domain structure of proteins from X-ray solution scattering.

Authors:  D I Svergun; M V Petoukhov; M H Koch
Journal:  Biophys J       Date:  2001-06       Impact factor: 4.033

3.  Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution.

Authors:  David A Jacques; J Mitchell Guss; Dmitri I Svergun; Jill Trewhella
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-05-17

Review 4.  Structural characterization of proteins and complexes using small-angle X-ray solution scattering.

Authors:  Haydyn D T Mertens; Dmitri I Svergun
Journal:  J Struct Biol       Date:  2010-06-15       Impact factor: 2.867

5.  Multidomain assembled states of Hck tyrosine kinase in solution.

Authors:  Sichun Yang; Lydia Blachowicz; Lee Makowski; Benoît Roux
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-23       Impact factor: 11.205

6.  Global rigid body modeling of macromolecular complexes against small-angle scattering data.

Authors:  Maxim V Petoukhov; Dmitri I Svergun
Journal:  Biophys J       Date:  2005-05-27       Impact factor: 4.033

Review 7.  Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

Authors:  Jill Trewhella; Wayne A Hendrickson; Gerard J Kleywegt; Andrej Sali; Mamoru Sato; Torsten Schwede; Dmitri I Svergun; John A Tainer; John Westbrook; Helen M Berman
Journal:  Structure       Date:  2013-06-04       Impact factor: 5.006

8.  Effects of macromolecular crowding on an intrinsically disordered protein characterized by small-angle neutron scattering with contrast matching.

Authors:  Daniel Johansen; Cy M J Jeffries; Boualem Hammouda; Jill Trewhella; David P Goldenberg
Journal:  Biophys J       Date:  2011-02-16       Impact factor: 4.033

9.  Policy: NIH plans to enhance reproducibility.

Authors:  Francis S Collins; Lawrence A Tabak
Journal:  Nature       Date:  2014-01-30       Impact factor: 49.962

10.  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.

Authors:  Helen Berman; Kim Henrick; Haruki Nakamura; John L Markley
Journal:  Nucleic Acids Res       Date:  2006-11-16       Impact factor: 16.971

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  116 in total

1.  Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure.

Authors:  David A Korasick; Harkewal Singh; Travis A Pemberton; Min Luo; Richa Dhatwalia; John J Tanner
Journal:  FEBS J       Date:  2017-08-01       Impact factor: 5.542

2.  Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

Authors:  Brinda Vallat; Benjamin Webb; John D Westbrook; Andrej Sali; Helen M Berman
Journal:  Structure       Date:  2018-04-12       Impact factor: 5.006

3.  pyDockSAXS: protein-protein complex structure by SAXS and computational docking.

Authors:  Brian Jiménez-García; Carles Pons; Dmitri I Svergun; Pau Bernadó; Juan Fernández-Recio
Journal:  Nucleic Acids Res       Date:  2015-04-20       Impact factor: 16.971

4.  Quaternary structure of α-amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) controls its activity.

Authors:  Yu Yang; Ian Davis; Tsutomu Matsui; Ivan Rubalcava; Aimin Liu
Journal:  J Biol Chem       Date:  2019-06-12       Impact factor: 5.157

5.  Solution structure and flexibility of the condensin HEAT-repeat subunit Ycg1.

Authors:  Karen Manalastas-Cantos; Marc Kschonsak; Christian H Haering; Dmitri I Svergun
Journal:  J Biol Chem       Date:  2019-07-26       Impact factor: 5.157

Review 6.  The role of small-angle scattering in structure-based screening applications.

Authors:  Po-Chia Chen; Janosch Hennig
Journal:  Biophys Rev       Date:  2018-10-10

7.  SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale.

Authors:  Vassili Piiadov; Evandro Ares de Araújo; Mario Oliveira Neto; Aldo Felix Craievich; Igor Polikarpov
Journal:  Protein Sci       Date:  2018-12-13       Impact factor: 6.725

8.  The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.

Authors:  Ashley J Winter; Christopher Williams; Michail N Isupov; Hannah Crocker; Mariya Gromova; Philip Marsh; Oliver J Wilkinson; Mark S Dillingham; Nicholas J Harmer; Richard W Titball; Matthew P Crump
Journal:  J Biol Chem       Date:  2018-10-18       Impact factor: 5.157

9.  Human Dystrophin Structural Changes upon Binding to Anionic Membrane Lipids.

Authors:  Raphael Dos Santos Morais; Olivier Delalande; Javier Pérez; Dominique Mias-Lucquin; Mélanie Lagarrigue; Anne Martel; Anne-Elisabeth Molza; Angélique Chéron; Céline Raguénès-Nicol; Thomas Chenuel; Arnaud Bondon; Marie-Sousai Appavou; Elisabeth Le Rumeur; Sophie Combet; Jean-François Hubert
Journal:  Biophys J       Date:  2018-08-17       Impact factor: 4.033

10.  RAID3--An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity.

Authors:  Florian Mittelberger; Cindy Meyer; Georg H Waetzig; Martin Zacharias; Erica Valentini; Dmitri I Svergun; Katharina Berg; Inken Lorenzen; Joachim Grötzinger; Stefan Rose-John; Ulrich Hahn
Journal:  RNA Biol       Date:  2015       Impact factor: 4.652

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