Literature DB >> 31576635

SASBDB: Towards an automatically curated and validated repository for biological scattering data.

Alexey G Kikhney1, Clemente R Borges1, Dmitry S Molodenskiy1, Cy M Jeffries1, Dmitri I Svergun1.   

Abstract

Small-angle scattering (SAS) of X-rays and neutrons is a fundamental tool to study the nanostructural properties, and in particular, biological macromolecules in solution. In structural biology, SAS recently transformed from a specialization into a general technique leading to a dramatic increase in the number of publications reporting structural models. The growing amount of data recorded and published has led to an urgent need for a global SAS repository that includes both primary data and models. In response to this, a small-angle scattering biological data bank (SASBDB) was designed in 2014 and is available for public access at www.sasbdb.org. SASBDB is a comprehensive, free and searchable repository of SAS experimental data and models deposited together with the relevant experimental conditions, sample details and instrument characteristics. SASBDB is rapidly growing, and presently has over 1,000 entries containing more than 1,600 models. We describe here the overall organization and procedures of SASBDB paying most attention to user-relevant information during submission. Perspectives of further developments, in particular, with OneDep system of the Protein Data Bank, and also widening of SASBDB including new types of data/models are discussed.
© 2019 The Protein Society.

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Year:  2019        PMID: 31576635      PMCID: PMC6933840          DOI: 10.1002/pro.3731

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  33 in total

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Journal:  Structure       Date:  2017-02-09       Impact factor: 5.006

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Authors:  Daniel Franke; Cy M Jeffries; Dmitri I Svergun
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6.  Ab initio electron density determination directly from solution scattering data.

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Journal:  Nat Methods       Date:  2018-01-29       Impact factor: 28.547

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Journal:  Nucleic Acids Res       Date:  2014-10-28       Impact factor: 16.971

8.  ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions.

Authors:  D Franke; M V Petoukhov; P V Konarev; A Panjkovich; A Tuukkanen; H D T Mertens; A G Kikhney; N R Hajizadeh; J M Franklin; C M Jeffries; D I Svergun
Journal:  J Appl Crystallogr       Date:  2017-06-26       Impact factor: 3.304

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Journal:  Nat Protoc       Date:  2015-05-07       Impact factor: 13.491

10.  Protein Data Bank: the single global archive for 3D macromolecular structure data.

Authors: 
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

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  40 in total

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2.  SASBDB: Towards an automatically curated and validated repository for biological scattering data.

Authors:  Alexey G Kikhney; Clemente R Borges; Dmitry S Molodenskiy; Cy M Jeffries; Dmitri I Svergun
Journal:  Protein Sci       Date:  2019-10-11       Impact factor: 6.725

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9.  Structural Insights of Shigella Translocator IpaB and Its Chaperone IpgC in Solution.

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10.  Order from disorder in the sarcomere: FATZ forms a fuzzy but tight complex and phase-separated condensates with α-actinin.

Authors:  Antonio Sponga; Joan L Arolas; Thomas C Schwarz; Cy M Jeffries; Ariadna Rodriguez Chamorro; Julius Kostan; Andrea Ghisleni; Friedel Drepper; Anton Polyansky; Euripedes De Almeida Ribeiro; Miriam Pedron; Anna Zawadzka-Kazimierczuk; Georg Mlynek; Thomas Peterbauer; Pierantonio Doto; Claudia Schreiner; Eneda Hollerl; Borja Mateos; Leonhard Geist; Georgine Faulkner; Wiktor Kozminski; Dmitri I Svergun; Bettina Warscheid; Bojan Zagrovic; Mathias Gautel; Robert Konrat; Kristina Djinović-Carugo
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