{"id":5248,"date":"2015-09-14T17:18:48","date_gmt":"2015-09-14T15:18:48","guid":{"rendered":"http:\/\/news.embl.de\/?p=5248"},"modified":"2024-04-19T15:38:36","modified_gmt":"2024-04-19T13:38:36","slug":"1509-sasbdb","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/","title":{"rendered":"From side-project to valuable resource"},"content":{"rendered":"\n

As a tool for gleaning information about the 3D atomic structure of proteins, Small Angle Scattering (SAS) is gaining in popularity and importance. As life scientists realise its potential, especially in combination with other structural biology approaches such as crystallography, so the amount of data being produced is increasing. The SASBDB is a repository for SAS data and models, and is presently the world\u2019s largest database for user-friendly storage and searching of SAS X-ray (SAXS) and Neutron (SANS) data.<\/p>\n\n\n\n

This is a really useful and much-needed resource for the SAS community<\/p><\/blockquote>\n\n\n\n

\u201cThis is a really useful and much-needed resource for the SAS community,\u201d explains Dmitri Svergun, head of the SAXS group in Hamburg<\/a> and Valentini\u2019s PhD supervisor. \u201cWith an increasing amount of SAS data becoming available, the need for a comprehensive repository has become quite urgent,\u201d he adds. \u201cWe are pleased we could address this need and can now present the database to the SAS community.\u201d Prior to the SASBDB, several SAXS models \u2013 often submitted alongside crystallographic data \u2013 were stored in the worldwide Protein Data Bank (wwPDB). Recognising that they did not have the expertise nor resources to adequately handle and curate the SAXS data, the wwPDB established a task force to draw up guidelines for a dedicated SAS data repository.<\/p>\n\n\n\n

A few years on, and scientists can now use the SASBDB to access and download data related to a SAXS\/SANS experiment, rather than just viewing an image of the model or scattering curve in a publication. Currently, the SASBDB is receiving new entries every few weeks, and slowly but surely the database is growing. \u201cWe are asking many of our collaborators to deposit their structures in the data bank and we hope that it will become standard practice, just like the PDB is standard for crystallographic data,\u201d explains Valentini. The SASBDB is now ready to receive the SAXS models that were previously stored in the wwPDB. \u201cWe have started doing tests and writing scripts to import the data,\u201d Valentini says. \u201cWe already have about 190 entries, and we are gearing up to take another 50 or so.\u201d<\/p>\n\n\n\n

It is crucial that we have access to comprehensive raw data from all SAS experiments so that these can always be referred to, reinterpreted and reanalysed.<\/p><\/blockquote>\n\n\n\n

\u201cIncreasingly, techniques other than crystallography, NMR and electron microscopy are being used by structural biologists to study complex biological systems,\u201d says Gerard Kleywegt, who heads the PDBe (Protein Data Bank in Europe)<\/a> hosted at EMBL-EBI, \u201cHybrid methods, where multiple techniques are used, are becoming more and more common.\u201d Kleywegt welcomes the launch of the SASBDB and the collaboration with wwPDB: \u201cHaving a major standard repository for each of these techniques is absolutely vital for scientists worldwide \u2013 as time goes on and methods develop, it is crucial that we have access to comprehensive raw data from all SAS experiments so that these can always be referred to, reinterpreted and reanalysed.\u201d If not otherwise communicated to the SASBDB team, entries will be published six months after submission.<\/p>\n\n\n\n

Remarkably, the database actually stemmed from a small side project, and put Valentini on the right path after a stumbling start to her PhD. \u201cOur collaborators were starting a database for storing experimental data from different techniques, including SAXS, and asked for our contribution,\u201d she explains. Svergun asked if she would like to be involved by providing them with some SAXS data \u2013 having studied databases as part of her Master\u2019s degree, Erica knew that in order to store data you needed to understand the structure behind it first. \u201cI drew a schema of what the database should look like \u2013 when Dmitri saw that I understood these things, we started to consider whether we could do something ourselves,\u201d she says. \u201cI feel really lucky with my PhD \u2013 Dmitri really understood my strengths and pushed me in the right direction.\u201d Now in the process of making plans to leave Hamburg, Valentini has had to step back from the project and hand the reins to colleagues within the SAXS group. \u201cIt\u2019s hard to let go of your baby,\u201d she smiles, \u201cbut I am really satisfied with how it has all worked out, and I will keep on watching it grow!\u201d<\/p>\n\n\n

\n

SASBDB facts and figures<\/h2>\n

– SASBDB is a searchable, curated repository<\/strong> of freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits.
\n – SASBDB currently contains almost 200 experimental data sets<\/strong> and approaching 300 models<\/strong>.
\n – The database includes 17 entries from well-characterised, highly purified proteins<\/strong>: examples of good data that can be used for teaching, learning and programming purposes.
\n – Almost 3000 new users<\/strong> from across the globe have accessed the website since its launch in August 2014.
\n – More than 700 entries have been downloaded<\/strong> since its launch.
\n – The SASBDB is maintained by the Biological Small Angle Scattering Group, EMBL Hamburg.
\n – For questions and feedback, contact: sasbdb@embl-hamburg.de<\/a>.
\n – Follow @svergungroup<\/a> on twitter for SASBDB news and updates. <\/p><\/div>\n","protected":false},"excerpt":{"rendered":"

Introducing the Small Angle Scattering Biological Data Bank, developed at EMBL Hamburg.<\/p>\n","protected":false},"author":18,"featured_media":5278,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[3,17591],"tags":[782,53,76,251,35,250],"embl_taxonomy":[],"class_list":["post-5248","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-lab-matters","category-science-technology","tag-database","tag-hamburg","tag-service","tag-small-angle-x-ray-scattering-saxs","tag-structural-biology","tag-svergun"],"acf":{"article_intro":"

With her PhD in her pocket, Erica Valentini is now ready to move onto the next stage of her career. But not before she has made sure the product of her PhD project \u2013 the Small Angle Scattering Biological Data Bank<\/a> or SASBDB for short \u2013 is in good hands. \u201cThe project really was my baby!\u201d she says with a wide grin. \u201cNow it\u2019s ready for the real world and is learning to walk!\u201d<\/p>\n","related_links":[{"link_description":"Small Angle Scattering Biological Data Bank","link_url":"http:\/\/www.sasbdb.org\/"},{"link_description":"Protein Data Bank in Europe","link_url":"http:\/\/www.ebi.ac.uk\/pdbe\/"},{"link_description":"Worldwide Protein Data Bank (wwPDB)","link_url":"http:\/\/www.wwpdb.org\/"},{"link_description":"Biological Small Angle Scattering Group, EMBL Hamburg","link_url":"http:\/\/www.embl-hamburg.de\/research\/unit\/svergun\/index.html"},{"link_description":"Nucleic Acids Res. 28 Jan 2015 doi: 10.1093\/nar\/gku1047 ","link_url":"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4383894\/"}],"article_sources":[{"source_description":"

Valentini\u00a0E, et al.\u00a0Nucleic Acids Research<\/em>, 28 Jan 2015. DOI:\u00a010.1093\/nar\/gku1047<\/p>\n","source_link_url":"http:\/\/dx.doi.org\/10.1093\/nar\/gku1047"}],"vf_locked":false,"featured":false,"color":"#007B53"},"embl_taxonomy_terms":[],"yoast_head":"\nFrom side-project to valuable resource | EMBL<\/title>\n<meta name=\"description\" content=\"Introducing the Small Angle Scattering Biological Data Bank (SASBDB), developed at EMBL Hamburg.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"From side-project to valuable resource | EMBL\" \/>\n<meta property=\"og:description\" content=\"Introducing the Small Angle Scattering Biological Data Bank (SASBDB), developed at EMBL Hamburg.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:published_time\" content=\"2015-09-14T15:18:48+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-04-19T13:38:36+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/09\/1509-sasbdb-ib.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"620\" \/>\n\t<meta property=\"og:image:height\" content=\"425\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Rosemary Wilson\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@rawilson80\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Rosemary Wilson\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"4 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/\"},\"author\":{\"name\":\"Rosemary Wilson\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/bb5e57a6c6c5c3b33a6a40b2d4c96e40\"},\"headline\":\"From side-project to valuable resource\",\"datePublished\":\"2015-09-14T15:18:48+00:00\",\"dateModified\":\"2024-04-19T13:38:36+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/\"},\"wordCount\":837,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/09\/1509-sasbdb-ib.jpg\",\"keywords\":[\"database\",\"hamburg\",\"service\",\"small-angle x-ray scattering (saxs)\",\"structural biology\",\"svergun\"],\"articleSection\":[\"Lab Matters\",\"Science & Technology\"],\"inLanguage\":\"en-US\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/\",\"url\":\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/\",\"name\":\"From side-project to valuable resource | EMBL\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/09\/1509-sasbdb-ib.jpg\",\"datePublished\":\"2015-09-14T15:18:48+00:00\",\"dateModified\":\"2024-04-19T13:38:36+00:00\",\"description\":\"Introducing the Small Angle Scattering Biological Data Bank (SASBDB), developed at EMBL Hamburg.\",\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.embl.org\/news\/lab-matters\/1509-sasbdb\/#primaryimage\",\"url\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/09\/1509-sasbdb-ib.jpg\",\"contentUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/09\/1509-sasbdb-ib.jpg\",\"width\":620,\"height\":425,\"caption\":\"Erica Valentini. 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