SASBDB Small Angle Scattering Biological Data Bank

Erica ValentiniDmitri Svergun group

Solution Scattering from biological macromolecules EMBO course 2014

1. Introduction:– What is SAS?

– Do we need a SAS database?

2. SASBDB:– Features

– Usage

– Quality check

– Missing

3. Conclusions

2SAS EMBO Course 201411/2/2014

– Usage

– Quality check

– Missing

3. Conclusions

What is SAS?SAS Experiment

|s| = 4π sinθ/λ

s scattering vector2θ scattering angleλ wavelengthI(s) intensity

X-ray/Neutron beam

Low resolution Model

Scattering In

tensity, Lo

g I(s)

What is SAS?ATSAS Package

Volume

Rigid bodymodelling

Missingfragments

Oligomericmixtures

FlexibleSystem

Do we need a SAS DB?SA(X)S advantages

Increasing popularity of SAXS

Solution

Broad size range

New developments

in software and hardware

From few kDa to GDa

Fast experiments: μor m seconds. Small amount of sample: 5-30 μl.

Monitor alteration in environmental conditions.

Do we need a SAS DB?SAS database motivations

7SAS EMBO Course 2014

• Increasing number of publications about SAS and the ATSAS package.

• Increasing amount of data collected with a single experiment.

• Importance of making the data underlying scientific publications available for the community.

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.

2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012

Number of publications referring to biological SAS

bioSAS

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Do we need a SAS DB?wwPDB SAS task force

SAS EMBO Course 2014 8

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.

“…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

SASBDB11/2/2014

Do we need a SAS DB?Existing DB including SAS data

Database SAS data included Missing

47 models where SAS was used for refinement

Primary data used to calculate the models

Scattering curves from 20.000 pdb structures

Models and possibility to deposit SAS data.

SAXS data and models Complete search, cross-references to other databases, quality check on data

Scattering curves and ensembles models fromdisordered proteins

SAS data and models from “not 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.

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dara.embl-hamburg.deSokolova, 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.

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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.

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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.

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– Usage

– Quality check

– Missing

3. Conclusions

SASBDB features:

1. Entries

2. Cross links

3. Searching

4. Browsing

5. Benchmark

6. Plots

7. Interactivity

8. Availability

SAS EMBO Course 2014 1511/2/2014

1. Entries

1. Entries2. Cross links3. Searching4. Browsing5. Benchmark6. Plots7. Interactivity8. Availability

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www.sasbdb.org

1. Entries

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2. Cross links

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3. Searching1. Simple search:

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3. Searching1. Simple search:

2. Advanced search:

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3. Searching

Browsing unit

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4. Browsing

Scattering curve

Kratky plot

Experiment information

Publication

Structural parametersUnique code

format: SASXXXN

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4. Browsing

Chronological order

Browse according to the selected field

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5. Benchmark

Benchmark

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5. Benchmark

• 17 Entries from a set of 14 “standard proteins”

• SAXS and WAXS data

• Extra purification steps

• Benchmark for algorithm testing proposes

• Dissemination

Dissemination

11/2/2014

6. Plots

Scattering plot

Guinierregion

Kratky plot

P(r) distribution

11/2/2014

vRadius of Gyration

Maximum Distance

MWs & Porod

Volume

vRadius of Gyration

6. Plots

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Fitting 1 Model 1

Fitting 2 Model 2

7. Interactivity

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Fitting 3 Model 1

Model 2

Model 3

Model 4

7. Interactivity

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Experim

details

lecule

details

7. Interactivity

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8. Availability

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8. Availability

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8. Availability

• Possibility to log in using ATSAS account

• Submission form

• Users can choose between:– “on hold”

– “public”

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– Usage

– Quality check

– Missing

3. Conclusions

SASBDB Usage

More than 500 users from August 2014We are currently monitoring also search items and number of downloads

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SASBDB Usage: use cases

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SAS userSAS novice Article referee

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11/2/2014 SAS EMBO Course 2014 38

11/2/2014 SAS EMBO Course 2014 39

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SAS EMBO Course 2014

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– Usage

– Quality check

– Missing

3. Conclusions

SASBDB Quality check:Difference Rg (Guinier) and Rg (p(r))

11/2/2014 SAS EMBO Course 2014 48

SASBDB Quality check:Difference Rg (Guinier) and Rg (p(r))

11/2/2014 SAS EMBO Course 2014 49

SASBDB Quality check:Difference MW (expected) and MW (experimental)

11/2/2014 SAS EMBO Course 2014 50

SASBDB Quality check:Quality p(r) distribution

11/2/2014 SAS EMBO Course 2014 51

SASBDB Quality check:Quality Guinier region

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SASBDB Quality check:Quality of the fit

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SASBDB Quality check:Quality of the data

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SASBDB Quality check:Quality of the data

11/2/2014 SAS EMBO Course 2014 55

SASBDB Quality check:

11/2/2014 SAS EMBO Course 2014 56

• Difference between structural parameters• Quality of the Guinier region• Quality of the p(r) distribution• Discrepancy between expected and experimental MW• Overall quality of the data• Goodness of fit of the model

Quality score based on the comparison between the selected entry and all the other entries.

– Usage

– Quality check

– Missing

3. Conclusions

SASBDB: missing

Network of SAS databases

Validation/Quality check

Pipeline to compare

values

Assessment of the

angular range

Difference between

curves

Validation of models

Standard format

sasCIF

Submission interface

Automatic

SASBDB: missing

Pipeline to compare

values

Assessment of the

angular range

Difference between

curves

Standard format

sasCIF

Automatic

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.

SASBDB: missing

Pipeline to compare

values

Assessment of the

angular range

Difference between

curves

Standard format

sasCIF

Automatic

Read, R.J., Adams, P.D., Arendall, W.B., III, Brunger, A.T., Emsley, P., Joosten, R.P., Kleywegt, G.J., Krissinel, E.B., Lutteke, T., Otwinowski, Z., Perrakis, A., Richardson, J.S., Sheffler, W.H., Smith, J.L., Tickle, I.J., Vriend, G., Zwart, P.H.. (2011) A new generation of crystallographic validation tools for the Protein Data Bank. Structure 19: 1395-1412.

11/2/2014

SASBDB: missing

Pipeline to compare

values

Assessment of the

angular range

Difference between

curves

Standard format

sasCIF

Automatic

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.

11/2/2014

SASBDB: missing

Pipeline to compare

values

Assessment of the

angular range

Difference between

curves

Standard format

sasCIF

Automatic

Konarev, P. and Svergun, D.I. (2014) Submitted.

11/2/2014

SASBDB: missing

Pipeline to compare

values

Assessment of the

angular range

Difference between

curves

Standard format

sasCIF

Automatic

Franke, D., Jeffries, C.M. and Svergun, D.I. (2014) Submitted.

11/2/2014

SASBDB: missing

Pipeline to compare

values

Assessment of the

angular range

Difference between

curves

Standard format

sasCIF

Automatic

Tuukkanen, A. and Svergun, D.I. (2015) In preparation.

11/2/2014

SASBDB: missing

Pipeline to compare

values

Assessment of the

angular range

Difference between

curves

Standard format

sasCIF

Automatic

Malfois, M. and Svergun, D.I. (2000) sasCIF: an extension of core Crystallographic Information File for SAS. J. Appl. Crystallogr., 33, 812–816.

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SASBDB: missing

Pipeline to compare

values

Assessment of the

angular range

Difference between

curves

Standard format

sasCIF

Automatic

Yang, H., Guranovic, V., Dutta, S., Feng, Z., Berman, H. M. & Westbrook, J. D. (2004). Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Cryst. D60, 1833-1839.

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– Usage

– Quality check

– Missing

3. Conclusions

SASBDB: Conclusions

• With 100 entries and 163 models SASBDB is currently the largest repository of SAS data available.

• Entirely browsable according to different criteria.• Highly flexible search.• Embedded Javascript to display interactive 3D models.• Set of SAXS and WAXS data from “standard proteins”.• Cross links to other biological databases.• Aimed at different types of users• Several validation methods under development.• Development of the standard format: sasCIF.• Network of interconnected SAS databases.• Paper about SASBDB in N.A.R. 2015 Database issue.

Thanks for your attention!

SASBDB Small Angle Scattering Biological Data Bank

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