SASBDB, a repository for biological small-angle scattering data

被引：242

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

来源：

NUCLEIC ACIDS RESEARCH | 2015年 / 43卷 / D1期

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

页码：D357 / D363

页数：7

共 33 条

[1] Activities at the Universal Protein Resource (UniProt) [J].

Apweiler, Rolf ;

Bateman, Alex ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Alpi, Emanuele ;

Antunes, Ricardo ;

Arganiska, Joanna ;

Casanova, Elisabet Barrera ;

Bely, Benoit ;

Bingley, Mark ;

Bonilla, Carlos ;

Britto, Ramona ;

Bursteinas, Borisas ;

Chan, Wei Mun ;

Chavali, Gayatri ;

Cibrian-Uhalte, Elena ;

Da Silva, Alan ;

De Giorgi, Maurizio ;

Dogan, Tunca ;

Fazzini, Francesco ;

Gane, Paul ;

Castro, Leyla Garcia ;

Garmiri, Penelope ;

Hatton-Ellis, Emma ;

Hieta, Reija ;

Huntley, Rachael ;

Legge, Duncan ;

Liu, Wudong ;

Luo, Jie ;

MacDougall, Alistair ;

Mutowo, Prudence ;

Nightingale, Andrew ;

Orchard, Sandra ;

Pichler, Klemens ;

Poggioli, Diego ;

Pundir, Sangya ;

Pureza, Luis ;

Qi, Guoying ;

Rosanoff, Steven ;

Saidi, Rabie ;

Sawford, Tony ;

Shypitsyna, Aleksandra ;

Turner, Edward ;

Volynkin, Vladimir ;

Wardell, Tony ;

Watkins, Xavier ;

Zellner, Hermann ;

Corbett, Matt .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D191-D198

[2] The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data [J].

Berman, Helen ;

Henrick, Kim ;

Nakamura, Haruki ;

Markley, John L. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D301-D303

[3] Biopython']python: freely available Python']Python tools for computational molecular biology and bioinformatics [J].

Cock, Peter J. A. ;

Antao, Tiago ;

Chang, Jeffrey T. ;

Chapman, Brad A. ;

Cox, Cymon J. ;

Dalke, Andrew ;

Friedberg, Iddo ;

Hamelryck, Thomas ;

Kauff, Frank ;

Wilczynski, Bartek ;

de Hoon, Michiel J. L. .

BIOINFORMATICS, 2009, 25 (11) :1422-1423

[4] NIH plans to enhance reproducibility [J].

Collins, Francis S. ;

Tabak, Lawrence A. .

NATURE, 2014, 505 (7485) :612-613

[5]

Deshpande N, 2005, NUCLEIC ACIDS RES, V33, pD233

[6] Automated acquisition and analysis of small angle X-ray scattering data [J].

Franke, Daniel ;

Kikhney, Alexey G. ;

Svergun, Dmitri I. .

NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT, 2012, 689 :52-59

[7] DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering [J].

Franke, Daniel ;

Svergun, Dmitri I. .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2009, 42 :342-346

[8] Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS) [J].

Graewert, Melissa A. ;

Svergun, Dmitri I. .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2013, 23 (05) :748-754

[9]

Guinier A., 1939, ANN PHYS-LEIPZIG, V12, P161, DOI DOI 10.1051/ANPHYS/193911120161

[10] Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS) [J].

Hura, Greg L. ;

Menon, Angeli L. ;

Hammel, Michal ;

Rambo, Robert P. ;

Poole, Farris L., II ;

Tsutakawa, Susan E. ;

Jenney, Francis E., Jr. ;

Classen, Scott ;

Frankel, Kenneth A. ;

Hopkins, Robert C. ;

Yang, Sung-jae ;

Scott, Joseph W. ;

Dillard, Bret D. ;

Adams, Michael W. W. ;

Tainer, John A. .

NATURE METHODS, 2009, 6 (08) :606-U83

← 1 2 3 4 →