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SASBDB Small Angle Scattering Biological Data Bank Erica Valentini Dmitri Svergun group Solution Scattering from biological macromolecules EMBO course 2014 Index 1. Introduction: What is SAS? Do we need a SAS database? 2. SASBDB:

  1. SASBDB Small Angle Scattering Biological Data Bank Erica Valentini Dmitri Svergun group Solution Scattering from biological macromolecules EMBO course 2014

  2. Index 1. Introduction: – What is SAS? – Do we need a SAS database? 2. SASBDB: – Features – Usage – Quality check – Missing 3. Conclusions 11/2/2014 SAS EMBO Course 2014 2

  3. Index 1. Introduction: – What is SAS? – Do we need a SAS database? 2. SASBDB: – Features – Usage – Quality check – Missing 3. Conclusions 11/2/2014 SAS EMBO Course 2014 3

  4. What is SAS? SAS Experiment s X-ray/Neutron 2θ beam |s| = 4π sin θ/λ s scattering vector 2θ scattering angle λ wavelength I(s) intensity Low resolution Scattering Intensity, Log I(s) Model ATSAS 11/2/2014 SAS EMBO Course 2014 4

  5. What is SAS? ATSAS Package R g MM Rigid body D max modelling Volume Shape Missing fragments Flexible Oligomeric System mixtures 11/2/2014 SAS EMBO Course 2014 5

  6. Do we need a SAS DB? SA(X)S advantages Fast experiments: μ or m seconds. Small amount of New sample: 5-30 μ l. developments From few in software Broad size and hardware kDa to GDa range Solution Monitor alteration in environmental conditions. Increasing popularity of SAXS 11/2/2014 SAS EMBO Course 2014 6

  7. Do we need a SAS DB? SAS database motivations • Increasing number of Number of publications referring to biological SAS publications about SAS 400 and the ATSAS package. 350 • Increasing amount of 300 data collected with a 250 single experiment. ATSAS • 200 Importance of making bioSAS the data underlying 150 scientific publications 100 available for the 50 community. 0 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 Graewert, M. a and Svergun, D.I. (2013) Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS). Curr. Opin. Struct. Biol. , 23 , 748 – 54. Franke, D., Kikhney, A.G. and Svergun, D.I. (2012) Automated acquisition and analysis of small angle X-ray scattering data . Nucl. . Instruments Methods Phys. Res. Sect. A Accel. Spectrometers, Detect. Assoc. Equip. , 689 , 52 – 59. Collins, F.S. and Tabak, L. a (2014) Policy: NIH plans to enhance reproducibility . Nature , 505 , 612 – 3. 11/2/2014 SAS EMBO Course 2014 7

  8. Do we need a SAS DB? wwPDB SAS task force “…a global repository is needed that holds standard format X-ray and neutron SAS data that is searchable and freely accessible for download” Database and small angle scattering experts Trewhella, J., Hendrickson, W.A., Kleywegt, G.J., Sali, A., Sato, M., Schwede, T., Svergun, D.I., Tainer, J.A., Westbrook, J. and Berman, H.M. (2013) Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB. Structure , 21 , 875 – 881. SASBDB 11/2/2014 SAS EMBO Course 2014 8

  9. Do we need a SAS DB? Existing DB including SAS data Database SAS data included Missing 47 models where SAS was Primary data used to used for refinement calculate the models Scattering curves from Models and possibility to 20.000 pdb structures deposit SAS data. SAXS data and models Complete search, cross-references to other databases, quality check on data Scattering curves and SAS data and models from ensembles models from “not disordered proteins” disordered proteins 11/2/2014 SAS EMBO Course 2014 9

  10. Do we need a SAS DB? Existing DB including SAS data Database SAS data included Missing 47 models where SAS was Primary data used to used for refinement calculate the models Scattering curves from Models and possibility to 20.000 pdb structures deposit SAS data. SAXS data and models Complete search, cross-references to other databases, quality check on data Scattering curves and SAS data and models from ensembles models from “not disordered proteins” disordered proteins Berman, H., Henrick, K., Nakamura, H. and Markley, J.L. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. , 35 , D301 – 3. 11/2/2014 SAS EMBO Course 2014 10

  11. Do we need a SAS DB? Existing DB including SAS data Database SAS data included Missing 47 models where SAS was Primary data used to used for refinement calculate the models Scattering curves from Models and possibility to 20.000 pdb structures deposit SAS data. SAXS data and models Complete search, cross-references to other databases, quality check on data Scattering curves and SAS data and models from ensembles models from “not disordered proteins” disordered proteins dara.embl-hamburg.de Sokolova, A. V, Volkov, V. and Svergun, D. I. (2003) Prototype of a database for rapid protein classification based on solution scattering data. Conference papers classification based on solution scattering data . 1 , 865 – 868. 11/2/2014 SAS EMBO Course 2014 11

  12. Do we need a SAS DB? Existing DB including SAS data Database SAS data included Missing 47 models where SAS was Primary data used to used for refinement calculate the models Scattering curves from Models and possibility to 20.000 pdb structures deposit SAS data. SAXS data and models Complete search, cross-references to other databases, quality check on data Scattering curves and SAS data and models from ensembles models from “not disordered proteins” disordered proteins Hura, G.L., Menon, A.L., Hammel, M., Rambo, R.P., Poole, F.L., Tsutakawa, S.E., Jenney, F.E., Classen, S., Frankel, K. a, Hopkins, R.C., et al. (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat. Methods , 6 , 606 – 12. 11/2/2014 SAS EMBO Course 2014 12

  13. Do we need a SAS DB? Existing DB including SAS data Database SAS data included Missing 47 models where SAS was Primary data used to used for refinement calculate the models Scattering curves from Models and possibility to 20.000 pdb structures deposit SAS data. SAXS data and models Complete search, cross-references to other databases, quality check on data Scattering curves and SAS data and models from ensembles models from “not disordered proteins” disordered proteins Varadi, M., Kosol, S., Lebrun, P., Valentini, E., Blackledge, M., Dunker, a K., Felli, I.C., Forman-Kay, J.D., Kriwacki, R.W., Pierattelli, R., et al. (2014) pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. Nucleic Acids Res. , 42 , D326 – 35. 11/2/2014 SAS EMBO Course 2014 13

  14. Index 1. Introduction: – What is SAS? – Do we need a SAS database? 2. SASBDB: – Features – Usage – Quality check – Missing 3. Conclusions 11/2/2014 SAS EMBO Course 2014 14

  15. SASBDB features: 1. Entries 2. Cross links 3. Searching 4. Browsing 5. Benchmark 6. Plots 7. Interactivity 8. Availability 11/2/2014 SAS EMBO Course 2014 15

  16. 1. Entries 2. Cross links 3. Searching 4. Browsing 1. Entries 5. Benchmark 6. Plots 7. Interactivity 8. Availability www.sasbdb.org 11/2/2014 SAS EMBO Course 2014 16

  17. 1. Entries 2. Cross links 3. Searching 4. Browsing 1. Entries 5. Benchmark 6. Plots 7. Interactivity 8. Availability 11/2/2014 SAS EMBO Course 2014 17

  18. 1. Entries 2. Cross links 3. Searching 4. Browsing 2. Cross links 5. Benchmark 6. Plots 7. Interactivity 8. Availability 11/2/2014 SAS EMBO Course 2014 18

  19. 1. Entries 2. Cross links 3. Searching 4. Browsing 3. Searching 5. Benchmark 6. Plots 7. Interactivity 8. Availability 1. Simple search: 11/2/2014 SAS EMBO Course 2014 19

  20. 1. Entries 2. Cross links 3. Searching 4. Browsing 3. Searching 5. Benchmark 6. Plots 7. Interactivity 8. Availability 1. Simple search: 2. Advanced search: 11/2/2014 SAS EMBO Course 2014 20

  21. 1. Entries 2. Cross links 3. Searching 4. Browsing 3. Searching 5. Benchmark 6. Plots 7. Interactivity 8. Availability Browsing unit 11/2/2014 SAS EMBO Course 2014 21

  22. 1. Entries 2. Cross links 3. Searching 4. Browsing 4. Browsing 5. Benchmark 6. Plots 7. Interactivity 8. Availability Structural Unique code parameters format: SASXXXN Model Scattering curve Experiment information Publication Kratky plot 11/2/2014 SAS EMBO Course 2014 22

  23. 1. Entries 2. Cross links 3. Searching 4. Browsing 4. Browsing 5. Benchmark 6. Plots 7. Interactivity 8. Availability Chronological order Browse according to the selected field 11/2/2014 SAS EMBO Course 2014 23

  24. 1. Entries 2. Cross links 3. Searching 4. Browsing 5. Benchmark 5. Benchmark 6. Plots 7. Interactivity 8. Availability Benchmark 11/2/2014 SAS EMBO Course 2014 24

  25. 1. Entries 2. Cross links 3. Searching 4. Browsing 5. Benchmark 5. Benchmark 6. Plots 7. Interactivity Dissemination 8. Availability • 17 Entries from a set of 14 “standard proteins” • SAXS and WAXS data • Extra purification steps • Benchmark for algorithm testing proposes • Dissemination 11/2/2014 SAS EMBO Course 2014 25

  26. 1. Entries 2. Cross links 3. Searching 4. Browsing 6. Plots 5. Benchmark 6. Plots 7. Interactivity 8. Availability Guinier Scattering region plot Kratky plot P(r) distribution 11/2/2014 SAS EMBO Course 2014 26

  27. 1. Entries 2. Cross links 3. Searching 4. Browsing 6. Plots 5. Benchmark 6. Plots 7. Interactivity 8. Availability vRadius of MWs & Gyration Porod Volume vRadius of Gyration Maximum Distance 11/2/2014 SAS EMBO Course 2014 27

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