EMBL-EBI Annual Scientific Report 2012

Gerard KleywegtPhD University of Utrecht, 1991. Postdoctoralresearcher, then independent investigator,University of Uppsala, 1992-2009. Co-ordinator,then Programme Director of the SwedishStructural Biology Network, 1996-2009.Research Fellow of the Royal Swedish Academyof Sciences, 2002-2006. Professor of StructuralMolecular Biology, University of Uppsala, 2009.At EMBL-EBI since 2009.appointed a dedicated PDBe Outreach Co-ordinator in 2012.We organised an expert workshop on emerging structuralbiology techniques, such as electron tomography, soft X-raytomography and 3D scanning-electron microscopy in orderto assess archiving needs and opportunities. In response toa recommendation of this workshop, PDBe will seek fundingand start pilot archives for these new types of data. We alsoco-organised the EMBO course on Computational StructuralBiology. We delivered 23 lectures and 17 training/outreachpresentations, and contributed to more than 20 publications.We published six Quips (interactive structure tutorials) andreleased a timely and informative article about Kobilka andLefkowitz’s Nobel Prize-winning structures.Future plansOur goal is to make PDBe the logical first stop on any questfor information about 3D molecular and cellular structure.To transform the structural archives into a truly usefulresource for biomedical and related disciplines, we willcontinue to focus our developments on: advanced services(e.g., PDBePISA, PDBeFold, PDBeMotif and the new PDBbrowsers); annotation, validation and visualisation of liganddata; integration with other data resources; validation andpresentation of information about the quality and reliability ofstructural data; and exposing experimental data in ways thathelp all users understand the extent to which the data supportthe structural models and inferences. In 2013 the new jointwwPDB deposition and annotation system will be tested andreleased. Much of the groundwork for a complete redesign ofthe PDBe website and search system as well as the PDB andEMDB entry pages has been carried out in 2012, and the newwebsite will be launched in 2013. This event will also markthe start of a publicity campaign to make non-expert usersof structures aware of the wealth of 3D structural informationavailable from PDBe.Selected referencesVelankar, S., et al. (2012) PDBe: Protein Data Bank in Europe.Nucleic Acids Res 40, D519-D524.Gore, S., et al. (2012) Implementing an X-ray validationpipeline for the Protein Data Bank. Acta Crystallogr D68,478-483.Figure 2. Visualisation and analysis of experimental data andvalidation information for NMR-derived entries in the PDB, usingprotein PA1076 from P. aeruginosa as an example (PDB entry 2k4v).Clockwise from top: NMR structure ensemble, coloured by domain;atoms with unusual chemical shift values shown as coloured spheres;violations of distance constraints shown as yellow lines betweenthe corresponding hydrogen atoms; visualisation of experimentaltorsion-angle constraints and violations; visualisation of residualdipolar coupling data; representative model, with residues colouredaccording to the Red/Orange/Green quality score assigned by theNRG-CING resource.Patwardhan, A., et al. (2012) Data management challenges inthree-dimensional EM. Nat Struct Mol Biol 19, 1203-1207.Berman, H.M., et al. (2012) The Protein Data Bank at 40:Reflecting on the Past to Prepare for the Future. Structure 20,391-396.2012 EMBL-EBI Annual Scientific Report39