1. EMBL-EBI Structural Proteomics Automatic Target Selection Gordon Whamond

2. EMBL-EBI Aim: Provide a resource that facilitates the automatic selection of potential targets for protein structure determination while minimising human interaction with the software (if required). Input: Raw amino acid sequence UniProt accession number UniProt accession number and a sequence range Output: Query sequence showing possible domains All candidates for structure determination Recommendation for which sequence to use Project Overview

3. EMBL-EBI Considerations Is there a known structure? Are there Classified Structural (CATH, SCOP) Domains? Are there Known Sequence (Pfam) Domains? Are there Predicted Structural (Gene3D, Superfamily) Domains? Do Domain Boundaries Conform to Secondary Structure Restrictions? Which Species has a Representative Domain that is the Most Compactly Folded? The core implementation needs to be extendible and easily maintainable.

4. EMBL-EBI The software is to be implemented using the Taverna workbench. This is a tool that can be used to formulate the workflow and implement each of the processes as distributed web services. Tom Oinn - http://taverna.sourceforge.net/ Taverna Advantages: Distributed computing reduces resource requirement. Easily extendible system Maintenance issues shifted to external providers Disadvantages: Learning curve Convincing service providers to adopt a standard format Maintenance issues shifted to external providers

5. EMBL-EBI Taverna The prototype workflow: When it is expanded to show all of the incorporated sub-workflows is quite complex Luckily Taverna can provide a top level view.

6. EMBL-EBI Taverna

7. EMBL-EBI Dealing With DAS

8. EMBL-EBI Taverna

9. EMBL-EBI Process Data Secondary Structure Elements: (Method not yet chosen) Sequence Domains: Pfam, Gene3D, Superfamily etc Protein Folding: RONN, FoldIndex, DisEMBL Rank Target Selection: Based on loop lengths, folding predictions, etc

10. EMBL-EBI Starting the Process

11. EMBL-EBI Monitoring Progress

12. EMBL-EBI Assess Data

13. EMBL-EBI Review Results

14. EMBL-EBI Extensibility Java Services Straightforward to provide as a web service using Tomcat and Axis WSDL (describing the service) can be generated automatically Legacy Software Any command line based tools can be wrapped into a web service using Soaplab For example the EMBOSS tools are already available

15. EMBL-EBI Extensibility Output Format: To ensure generic service compatibility it helps to define a common results format. As a result we are using the e-Family service schema ( http://www.efamily.org.uk/) Current collaborators include: The Weizmann Institute - FoldIndex University of Oxford - RONN

16. EMBL-EBI http://www.efamily.org.uk/software/dasclients/spice/ Results Viewers

17. EMBL-EBI Conclusions Taverna and Web Services: Taverna facilitates the provision of complex distributed systems that utilise web services This reduces maintenance overheads and keeps technology requirements at a reasonable level It is also easily extensible to accommodate new services Availability: Hopefully the core system will be ready by the end of the year This will provide the basic workflow for users to customise according to their needs

18. EMBL-EBI Acknowledgments Thanks to: Tom Oinn Andreas Prlic The RONN and FoldIndex teams The MSD Group