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Gerard J. Kleywegt

Abstract

"Just because it's in Nature, doesn't mean it's true..."

To err is human, and all structural biologists are human - therefore, they are not immune to making errors during 3D model building and refinement [1]. Fortunately, many errors can be detected and fixed prior to publication and deposition by using common sense [1], appropriate protocols [2] and validation procedures [3].

In my lecture, I will discuss why errors are made and why some of them persist in published and deposited models, and hence why validation of 3D structure models is so important. I will describe what validation entails (both in general and for protein crystallography specifically) and explain why some validation criteria are more informative than others [4].

I will also discuss how the organisations that manage the global biomacromolecular structure resources (wwPDB and EMDataBank) address the issue of validation. The use of comprehensive validation procedures by these resources will hopefully lead to fewer errors going undetected. Moreover, information about the quality of PDB and EMDB entries will be invaluable for structure users, many of whom are not experts in experimental structural biology [5]. However, challenges for the validation-research community remain, in particular in validating low-resolution models (X-ray, EM, SAXS) and hybrid models based on multiple heterogeneous sources of both experimental data and fitted models.

[1] G.J. Kleywegt & T.A. Jones, "Where freedom is given, liberties are taken", Structure 1995, 3, 535-540.
[2] G.J. Kleywegt & T.A. Jones, "Model-building and refinement practice", Methods in Enzymology 1997, 277, 208-230.
[3] G.J. Kleywegt, "Validation of protein crystal structures", Acta Crystallographica 2000, D56, 249-265.
[4] G.J. Kleywegt, "On vital aid: the why, what and how of validation", Acta Crystallographica 2009, D65, 134-139.
[5] S. Velankar & G.J. Kleywegt, "The Protein Data Bank in Europe (PDBe): bringing structure to biology", Acta Crystallographica 2011, D67, 324-330.

Professional carreer

PhD, University of Utrecht, 1991. Postdoctoral researcher, then independent investigator, University of Uppsala, 1992-2009. Coordinator, then Programme Director of the Swedish Structural Biology Network, 1996-2009. Research Fellow of the Royal Swedish Academy of Sciences, 2002-2006. Professor of Structural Molecular Biology, University of Uppsala, 2009. At EMBL-EBI since 2009 as Senior Team Leader and Head of the Protein Data Bank in Europe.

E-mail: gerard@removethis.ebi.ac.uk

Phone: +44 - 1223 - 49 26 98 (PA)