Structural bioinformatics and ELIXIR UK by Christine Orengo
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The document outlines initiatives aimed at improving training in structural bioinformatics across Europe, led by Genome3D and supported by various academic institutions. It details workshops that identified training needs for different audiences, from clinical researchers to computational chemists, and developed plans to fill identified gaps in structural bioinformatics training. Future steps include further surveys, establishing a working group, and securing funding to implement comprehensive training workflows and resources.
Structural bioinformatics and ELIXIR UK by Christine Orengo
- 1. European Life Sciences Infrastructure for Biological Information www.elixir-‐europe.org Cath Brooksbank, EMBL-‐EBI Christine Orengo, UCL Structural bioinformatics training for ELIXIR-‐UK
- 2. Structural Bioinformatics Residues in contact with protein partner Active site <10% human proteins known structure ~70-80 can predict structures
- 3. 3 Genome3D are coordinating the ELIXIR Structural Bioinformatics Sector in collaboration with Cath Brooksbank at EBI Protein structure classification/analysis Alexey Murzin – LMB (Cambridge) -‐ SCOP Christine Orengo – UCL -‐ CATH Structural annotation of genome sequences and 3D models Tom Blundell – Cambridge University -‐ FUGUE Christine Orengo – Gene3D Julian Gough – Bristol University -‐ SUPERFAMILY David Jones – UCL -‐ pDomThreader Michael Sternberg – Imperial, London -‐ PHYRE Established 2010 with BBSRC funding -‐ http//:genome3d.eu
- 4. Our remit… (i) representing the sector at initial Training the Trainers (TTT) events (ii) organisation of an initial workshop that performs a training gap analysis for the sector (iii) fund-‐raising for resources that aim to plug these training gaps. 4 6 months part-‐time funding from the BBSRC Richard Grandison at the EBI working with Sarah Morgan and Cath Brooksbank at Train Online, EBI
- 5. Achieved so far… Survey of 100 UK groups who need or deliver training in structural bioinformatics 2 day workshop at the EBI – established a ‘Training Network’ and champions in 8 themes Questionnaire and notification of our training network sent to 60 major european groups in structural bioinformatics to identify training material 4 meetings to review existing training material, identify gaps and plan mechanisms for organising the data 5
- 6. Purpose of the Workshop • To reach agreement on the training needs of our target audiences: • clinical researchers • bench-‐based molecular life scientists • structural biologists • structural bioinformaticians • computational chemists (industry) • medicinal chemists (industry) • To develop a plan of how to meet these needs 6
- 7. Two-‐day workshop (February 2014) Target audiences and their needs Gaps in structural bioinformatics training and how to fill them Opportunities going forward • Divided audiences in to two groups: -‐ Generalists -‐ clinical researchers, molecular life scientists, medicinal chemists -‐ Specialists -‐ structural bioinformaticians, structural biologists, computational chemists 25 attendees, 3 breakouts
- 8. What are the common learning needs of the target audience • How is the quality of a protein structure reported • How can you predict the structure of a protein if the structure has not been determined • How can you assess the quality of a predicted structure • What can be inferred from a protein structure at different levels of quality eg • Impacts of a mutation on the stability or function • Affinity for a particular ligand 8
- 9. Two-‐day workshop (February 2014) Established a ‘structural bioinformatics network’ with thematic areas and champions for each area. Structural biology Protein structure prediction Protein protein complexes Protein ligand Interactions Structure-‐based sequence analysis Structure comparison/analysis Structure to function Molecular dynamics Sameer Velankar, Roman Laskowski Mike Sternberg, David Jones Franca Fraternali, Sarah Teichmann John Overington, Edith Chan Geoff Barton, Jim Proctor Christine Orengo, Alexey Murzin Mark Wass, Janet Thornton Francesco Gervasio
- 10. Structural Bioinformatics Sector Activities January : designed survey of needs sent to 200 groups across the UK February (EBI) : 2-‐day workshop, 25 participants April (UCL) : reviewed training material, designed a survey to identify further material, sent to 60 European groups (30 responses) June (EBI) : reviewed training material, identified gaps, planned training workflows August (UCL) : detailed design of workflows and metadata for TESS, Niall Beard from TeSS present October (UCL) : sample training workflow complete, request for funding planned 10
- 11. Analysis of Existing Training Material Structure annotation : PDB and TrainOnline Homology modeling : undergrad material; SWISS-‐MOD Structure prediction : significant gaps Protein interactions/docking : significant gaps Protein ligand docking : significant gaps Impacts of genetic variations : significant gaps 11
- 12. protein network Search protein(s) and interactions Database Integration Specific applications 3D structure tutorial tutorial tutorial link link tutorial link Interactome3D with structure / model? STRING Yes No Visualisation & Functional annotation tutorial Interface analysis tutorial tutorial tutorial Protein-protein interaction network analysis PDBePISA HOTREGION Complex prediction BLAST Structural analysis Output *BLAST: Basic Local Alignment Search Tool (sequence similarity) link
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- 15. Metadata on Training Material for TESS aggregator 15 Resource link tutorial paper URL inputs outputs endorsements • citations (age) • grading (elementary, medium, advanced) • traffic lights
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- 17. What are the next steps……. • Discussions with TeSS team on how the metadata is integrated in the platform • Continue to survey material and design the workflows • Establish a broader working group across europe (already in discussion with Torsten Schwede, Gert Vriend, others) • Discussion with BBSRC and other funding agencies to obtain funds to take the work forward • We need an 18 month post who will work with champions in each theme to build the workflows and populate the metadata tables • Another survey of industry, medical researchers, experimental biologists 17