SASBDB, a repository for biological small-angle scattering data

被引:238
|
作者
Valentini, Erica [1 ]
Kikhney, Alexey G. [1 ]
Previtali, Gianpietro [1 ]
Jeffries, Cy M. [1 ]
Svergun, Dmitri I. [1 ]
机构
[1] European Mol Biol Lab, Hamburg Outstn, D-22603 Hamburg, Germany
关键词
PROTEIN DATA-BANK; COMPLEXES; WWPDB; SAXS;
D O I
10.1093/nar/gku1047
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:D357 / D363
页数:7
相关论文
共 50 条
  • [1] Validation of biological small-angle scattering data and models in SASBDB
    Kikhney, Alexey
    Jeffries, Cy M.
    Borges, Clemente R.
    Hajizadeh, Nelly
    Manalastas, Karen K.
    Svergun, Dmitri I.
    [J]. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2017, 73 : C1440 - C1440
  • [2] SASBDB: Towards automatically curated and validated repository for biological scattering data
    Kikhney, Alexey G.
    Borges, Clemente R.
    Molodenskiy, Dmitry S.
    Jeffries, Cy M.
    Svergun, Dmitri I.
    [J]. PROTEIN SCIENCE, 2020, 29 (01) : 66 - 75
  • [3] SMALL-ANGLE SCATTERING OF BIOLOGICAL STRUCTURES
    STUHRMANN, HB
    MILLER, A
    [J]. JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1978, 11 (OCT) : 325 - 345
  • [4] On the role of small-angle scattering in biological research
    Moore, P.B.
    [J]. Journal of Applied Crystallography, 1988, 21 (06): : 675 - 680
  • [5] SMALL-ANGLE LIGHT SCATTERING BY BIOLOGICAL CELLS
    MULLANEY, PF
    VANDILLA, MA
    DEAN, PN
    [J]. BIOPHYSICAL JOURNAL, 1969, 9 : A77 - &
  • [6] Quantification of the information in small-angle scattering data
    Pedersen, Martin Cramer
    Hansen, Steen Laugesen
    Markussen, Bo
    Arleth, Lise
    Mortensen, Kell
    [J]. JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2014, 47 : 2000 - 2010
  • [7] Bayesian Inference for Small-Angle Scattering Data
    Hayashi, Yui
    Katakami, Shun
    Kuwamoto, Shigeo
    Nagata, Kenji
    Mizumaki, Masaichiro
    Okada, Masato
    [J]. JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 2023, 92 (09)
  • [8] THE ELLIPTICAL AVERAGE OF SMALL-ANGLE SCATTERING DATA
    REYNOLDS, LE
    MILDNER, DFR
    [J]. JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1984, 17 (DEC) : 411 - 416
  • [9] Small-angle scattering studies of biological macromolecules in solution
    Svergun, DI
    Koch, MHJ
    [J]. REPORTS ON PROGRESS IN PHYSICS, 2003, 66 (10) : 1735 - 1782
  • [10] NEUTRON SMALL-ANGLE SCATTERING OF BIOLOGICAL MACROMOLECULES IN SOLUTION
    STUHRMANN, HB
    [J]. JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1974, 7 (APR1): : 173 - 178