CING Validation Tools for Biomolecular NMR Structures Jurgen F. Doreleijers & Geerten W. Vuister Protein Biophysics, IMM & CMBI Radboud University Nijmegen.

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Presentation transcript:

CING Validation Tools for Biomolecular NMR Structures Jurgen F. Doreleijers & Geerten W. Vuister Protein Biophysics, IMM & CMBI Radboud University Nijmegen

sIMMposium ’09 Overview Intro NMR & Motivation Overview CING Applications 3 Wrong Structures iCing interface NRG-CING >4,000 eNMR ’09 Competition

sIMMposium ’09 Introduction Structural Biology by NMR Preparation t1t1 t1t1 t1t1 t2t2 Mix Mix1 Mix2 t3t3 t3t3 Mix3 t4t4 2D 3D 4D t2t2 t2t2 Spectroscopy DataStructures Interactions Dynamics Molecular Biology Biological question ?

sIMMposium ’09 Motivation NMR structures are generally not very good ~25 % of recently deposited structures is seriously flawed Structural quality can often be improved by: Proper computational procedures Validation of input data Validation of results Analysis of ~600 recent NMR SG structures 10%50%90% Nabuurs et al. PLoS Comp. Biol. 2, e9, 2006 Volkskrant ‘06

sIMMposium ’09 Common errors in NMR structures Global Folds. Packing. Local Geometry. H-bonds and Electrostatics. Agreement with Experimental Data.

sIMMposium ’09 Traditional NMR validation Programs e.g.: PROCHECK_NMR WHAT IF Insufficient to use in isolation. Difficult to work with. No relation between results. More checks are possible.

sIMMposium ’09 Overview Intro NMR & Motivation Overview CING Applications 3 Wrong Structures iCing interface NRG-CING >4,000 eNMR ’09 Competition

sIMMposium ’09 Common Interface for NMR structure Generation

sIMMposium ’09 Overview CING User friendly interface to external program’s results and reports (WHAT IF/PROCHECK_NMR/Aqua/SHIFTX/Wattos/DSSP/etc.) Residue oriented Validation and data together Hyperlinked HTML ROG coded (red, orange, green) (ROG-score) Smart and guide user to troublesome areas!

sIMMposium ’09 CING is Part of EU Pipeline for NMR nmr.eu nmr.eu

sIMMposium ’09 Overview CING: Data flow Aqua Wattos DSSP

sIMMposium ’09 ROG score Criteria Molecule Chain Residue Atom Chemical shift, Restraint, Peak or List thereof

sIMMposium ’09 CING: project page Links to relevant elements

sIMMposium ’09 CING: molecule page Links to residues Color coding Easy navigation

sIMMposium ’09 CING: residue page Critiques

sIMMposium ’09 CING: residue page

sIMMposium ’09 Overview Intro NMR & Motivation Overview CING Applications 3 Wrong Structures iCing interface NRG-CING >4,000 eNMR ’09 Competition

sIMMposium ’09 CING: Three Wrong Structures (1) 1Y4O 1TGQ red: 52 (54%) orange: 29 (30%) green: 15 (16%) red: 34 (16%) orange: 57 (27%) green: 117 (56%) Dynein Light Chain CESG versus NESG

sIMMposium ’09 CING: Three Wrong Structures (2) 2PP4 red: 25 (23%) orange: 36 (34%) green: 46 (43%) 2H7B red: 48 (46%) orange: 44 (42%) green: 13 (12%) TAF homology domain

sIMMposium ’09 CING: Three Wrong Structures (3) 1HKT; DBD Heat shock TF Vuister et al, 1994 red: 67 (63%) orange: 20 (19%) green: 19 (18%)

sIMMposium ’09 Overview Intro NMR & Motivation Overview CING Applications 3 Wrong Structures iCing interface NRG-CING >4,000 eNMR ’09 Competition

sIMMposium ’09 iCing web interface to CING

sIMMposium ’09 NRG-CING Converted NRG NMR restraints (collaboration with BMRB in Madison, WI, USA) 4,102 PDB Entries (>90 % of 4,411)

sIMMposium ’09 NRG-CING problematic fine red (%) green (%)

sIMMposium ’09 NRG-CING 1AQ5

sIMMposium ’09 NRG-CING 1R48

sIMMposium ’09 NRG-CING 1HY8

sIMMposium ’09 NRG-CING ROG green (%) Old criterium (PC most favorite) (%)

sIMMposium ’09 eNMR Competition May 2009 nmr.cmbi.ru.nl/eNMRworksho p 51 new datasets

sIMMposium ’09 eNMR results CheshireFrankfurtLyonParisPiscataway, USAUtrecht

sIMMposium ’09 eNMR results

sIMMposium ’09 eNMR results

sIMMposium ’09 eNMR results

sIMMposium ’09 eNMR results

sIMMposium ’09 eNMR results

sIMMposium ’09 eNMR results

sIMMposium ’09 Conclusions Proper validation of structural quality in relation to the experimental data is essential. Error detection should be an integral part of the computation/validation process. Use of any global validation parameters as a quality indicator appears to be useless. We therefore advocate a residue-specific validation. CING provides for: a flexible API for the structure ensemble, experimental data, and the validation results. allows for an integrated, comprehensive residue-specific validation approach, that can detect misfolded structures as well as local problems.

sIMMposium ’09 Credits

Credits Protein Biophysics (IMM) and CMBI, Radboud University Nijmegen CING authors Geerten Vuister (Protein Biophysics) Alan Wilter S. da Silva (CCPN, Cambridge) CING contributing authors Sander Nabuurs (CMBI) Chris Spronk ( Gert Vriend (CMBI) Elmar Krieger (YASARA, Tim Stevens (CTim Stevens (CCPN, Cambridge)Funding NWO-CW VICI & EXTEND-NMR